my journey begins and never ends

if the gasket is actual metal, it should be fine to grind it out to shape, with a dremel or the like.

for porting the intake and exhaust, its waaaaaaaaaaaaay easier to do it from the outside of the jug.
the transfer ports... not so easy. :s
i dont have a method to do them as of yet, the tools i use are works gear. and the die grinder bit is much too large for them. works great for the bottom end though.
gotta watch WHERE you take off , and how MUCH you take off the intake and exhaust... they WILL effect the operation of the engine!!


speaking of bottom end... thats where a lot of the bottlenecking comes from.
at very least, match it to the jug.
easiest way to do so is to split the case, and match jug. each side.

Nice job on the poston, those little scuffs on the piston skirt aren't that bad and can be fixed by removing any high metal with a jewelers file or some fine sandpaper, just need to remove any metal that protrudes above the surface, the indentations won't hurt anything. If there was a deep scratch tho, it would need to be blended out but those little nicks won't hurt it.

The lower transfer openings are looking good too

As far as greasing certain parts during the rebuild process, about the only parts that need grease are the bevel and clutch gears, the clutch cam and the bucking bar and ball, you'll get all kinds of opinions on marine grade, Lucas red n tacky, moly greases, and lithium greases.... Of all the ones I've tried over the years, my preference is Kendall super blu, it's a lithium complex grease that's water proof and it's not super sticky like the red greases but it stays put just as well. This stuff works great for the gears and the clutch parts like the clutch cam, bucking bar and ball. If you prefer the red sticky grease, it does work good on the gears since it stays put and it's really thick so it helps quiet the gears a little, but the gears will usually quiet down on their own after the bike has been run for about an hour or so.
You don't need a lot of grease on the gears tho and it can't come in contact with the clutch pads, just a small dab on the gear and it'll spread over all the teeth quickly once run.
This is the stuff I use on everything from the bevel gears and clutch parts as well as the brake and clutch cables on these bikes to the bearings in high end cars or heavy duty trucks... it's just a really good all around grease, it's waterproof, it stays put, and it protects the parts very well, even after 30k miles in a bearing it still looks like it was applied yesterday... http://www.petroleumservicecompany.com/kendall-super-blu.html the stuff can be hard to find sometimes but I get it off eBay in 1lb tubs for about $6 per tub and a 1lb tub will last about 3 to 6 months at the shop so it would last year's in one's garage...
Here's the ebay link I get it from if interested... http://www.ebay.com/itm/141658016531?_trksid=p2057872.m2749.l2649&ssPageName=STRK:MEBIDX:IT

There's no need to grease anything inside the engine but a thin coat can be applied if an engine is to be built then stored for a really long time to prevent corrosion, it'll keep things like new until the engine is ready to use then the fuel/oil mix will wash it out as the engine runs for the first few minutes, this step isn't needed unless the engine has to sit for several months unused in a very humid environment. Otherwise just a small amount of motor oil on the bearings and rings will be ok, the motor oil will stay put and protect the bearings etc for several weeks inside a closed engine. Some people will spray a shot of wd40 into the cylinder before starting for the first time just to lube the rings until the fuel oil mix can get in there.

That exhaust port looks Nice!!
Good job... did you measure how wide it is in the cylinder and at the outlet?
That's one of the better looking ports ive seen in here for sure, just be sure to keep it 29mm or less to prevent any chances of ring snagging. Not sure if you read about the 60% rule, but it means that as long as you don't go more than 60% of the bore diameter you wont run the risk of snagging a ring. You can also raise the port roof by 1mm for more rpm,but use a spare piston and ramp it to see how it performs before raising the roof higher. Basically, ramping the piston does the same effect as raising the port roof so its a good way to experiment without going too far on a cylinder. Mine usually come out where I want them with the roof raised about 2mm but that's also really close to where it effects the low rpm torque more and more.
Ramping the piston at the transfers is the best way to get more transfer duration since raising the transfer roofs effects blowdown and will take away low rpm performance because of residual exhaust pressure can push the fresh intake charge back down the transfers if the roof is too high, this can be remedied to a certain extent by case stuffing but really good performance can be had without stuffing the case by keeping track of the blowdown and not going too excessive so ramping the piston at the transfer openings only is an easy alternative, more power can still be had by stuffing the case but as long as your not too greedy with the transfer duration you can get away with excellent performance and not have to stuff the cases to prevent the exhaust pressure from overcoming the transfer pressure. A nice wide exhaust port like what you did also helps bleed off this pressure well before the transfer ports are exposed.
You're definitely doing a good job with it so far. If you have a degree wheel and a dial indicator that'll help you set the cylinder at just the right hight for best port timing and duration when you get closer to ready to put the cylinder back onto the bottom end... I have a few posts in here showing how I made the degree wheel and mount it to the crank but we can go over that when you're ready.

Yeah, the wide ports are good for making lots of torque...
You can do the intake but leave the surface rough... 80 or 100 grit sanding drum will leave a rough enough surface or just use the rotary files and don't polish which leaves a rough enough finish.just widen the intake 1mm on each side for excellent torque. You can also shave down the head using the sandpaper on glass method or if you got a belt/disc tabletop sander it'll make short work shaving down a head. I did a customer's engine by just widening the intake and exhaust ports then shaved down the stock head for better compression and better gasket sealing and that engine was a torque Monster... strong enough to slip the clutch on pavement or spin the wheel on dirt or gravel. The top speed was around 30 mph but the torque and acceleration was awesome.
Also, for good torque there's no need to raise the exhaust port roof or ramp the piston at the exhaust port, if you already did this tho it wont hurt since that exhaust port is nice and wide. You'll also want to sit your cylinder closer to the bottom end by using a thinner base gasket so the port duration is narrow but the air can get into and out of the engine in large volumes. A straight pipe that's longer will also help make lots of torque so you can extend the stock pipe or get onenof those really long poo poo pipes, this will also make the ride quieter since the noise will be behind you, and using a stock type muffler with 4 extra 5/16" holes drilled into the end cap will help make torque as well as keeping things quiet since we're not going to mess with the internal baffling.
if you choose to use an expansion chamber pipe you'll want a nice long header to keep the power down low. You can get a lot of torque out of these engines by using these tricks while keeping it nice and quiet, and still be able to do at least 30 mph or so on top.

well well.. you been busy mister!! haha!

looks great! keep it up :O)

ok, so first.... DONT .. i repeat DO NOT get the motocross poopoo pipe.
it is HORRIBLE! i had one, put it on... lost all tourqe, and top speed. And the back pressure blew out both seals. its only MAYBE 1/2" hose all the way thru.

to lap the head and jug top...
https://youtu.be/cQHdXcqAo-k

and watch the length of the spark plug. especially if your running a 40mm stroke engine. dont wanna smash the head off on first start

I agree about the spark plug... better to get the compression from shaving down the head or getting a high compression head and stick with the proper plug... a piston can hit a plug that's got too much reach.
As far as the poo poo pipe... if its a small diameter pipe then it could do more harm than good...the stock pipe does perform once the end cap has extra holes drilled, but also the flange on the stock pipe leaves a lot to be desired as the hole in the flange is even smaller than the stock exhaust port in the head. Ive port matched stock pipes which helps bring them around but the opening can only be brought up to the pipe's inner diameter or just slightly more if the weld is thick enough.
A straight pipe can also be fabricated out of 1˝ emt tubing (electrical conduit tubing) to give the pipe length and get the noise behind you, this will require welding or brazing a flange to the pipe or to splice the stock pipe in. The longer pipe will also contribute to more engine torque, and a longer intake will make more torque as well, but at the cost of some top end rpm.
Just using the stock pipe with extra holes in the end cap is an easy way to get better torque from the engine too, and a tuned expansion chamber would give the best gains but a straight pipe tuned to the right length can work quite well...

For the stripped screw head, you can most likely coax it out if you have an impact driver. You can get one with a bit set from most auto parts stores for fairly cheap, just make sure it's set in reverse before striking it with the hammer. This tool is a very good investment for anyone working on these or on motorcycles... or basically anything that's aluminum or die cast metal that has standard or phillips screws holding it together...

As for the pipe, that bike I built for a customer, I just used the stock pipe but drilled 5 5/16" holes thru the end cap and didn't even mess with the inner baffles. The engine was still nice and quiet after the holes were drilled but the torque was amazing combined with the mild port job I did, that engine was basically ports widened 1mm on each side of the intake and exhaust ports, head shaved down 1mm, casting ridge removed from transfer roofs, and I ramped the piston at the transfer openings only and cut 5mm off thte skirt on the intake side... took me all of about 30 minutes to do the port work, I didn't want it to be a screamer but since this customer was on the heavy side I did want better torque, but didn't expect it to make the crazy amount of torque it did, I was expecting it to be a little stronger but it turned out a LOT stronger and was still able to get above 30mph on top.
Yours should have similar or better torque with that really wide exhaust port if you can also get similar compression