Piston and manifold mods with pixs

Not bad on the piston, intake, and exhaust... It does take some practice, but I've seen a lot worse...
A few things that'll help even more would be to get a shorty intake and open it up on the inside to match the venturi diameter of the carb, the stock intakes are only 13mm on the inside so even putting on a bigger carb won't help performance very much, but there are some shorty intakes on ebay that can be opened up, and there are some aftermarket ones that are already open enough to take full advantage of the carb.
The banana pipe is ok bet it's designed to run best at rpm's these engines just can't reach, and they also have a very small and restrictive stinger so they're also restrictive. You can wake one of these up by cutting it so the outlet is atleast 16mm or more, 1" on the outlet is about as big as you would want to go. On the other side, you can cut the flange off but leave enough metal on the flange to weld in a section of steel pipe, then use a section of silicone hose the same diameter that's about a foot long, then take it for a spin, then trim it down until it hits where it'll work best for you and weld in a section of steel pipe to replace the silicone you were using for experimenting.... It's probably easier and more practical to get an SBP pipe or snake pipe and be done with it, but if on a really tight budget, the banana pipe could be modded to work a lot better.

The piston looks good and you cut about the right amount off the bottom of the skirt for better intake duration, the ramping on the exhaust looks ok, but should taper in about 1/2" and be about 1 to 1.5mm lower than the rest of the top of the piston at the exhaust port. Once you get your dremel going again, ramping the transfers down the same amount will make a noticeable difference too. You'll get the best torque increase tho by widening the actual exhaust and intake ports. Just going 1mm wider on each side will make a noticeable difference, raising the roof of the exhaust 1 to 2mm will also make a noticeable difference but the power will come on at a higher rpm if you take off too much from the roof. For the transfers, just getting rid of that casting ridge on the roof is all that's usually needed, you don't want to raise the transfer roofs, but can ramp the piston at the transfer openings. Then knife edge the transfer openings at the bottom of the cylinder, this really helps. I go a lot further with porting the transfers but don't mess with the actual openings inside the cylinder, they're really good where they're at, and raising the roof any could really kill off the power because they could open before all the exhaust pressure is bled off... not good... But you can get a bit more power and smoothness by removing that casting ridge.
For the head, I don't know if you messed with it yet, but shaving off at least 1mm from the gasket mating surface will give you more compression and a good boost thruout the rpm range, just use a sheet of sandpaper on a glass surface and sand it down until at least 1mm is taken off, this will also help with head gasket sealing since these arent very flat right out of the box. Getting a Puch or Fred head will also help with compression, but also help keep the engine cool as the stock head doesn't do a very good job keeping a performance engine cool.

Anyway, good work so far and if you need to know anything else on how to make it fast, just ask.
As far as your engine vibrating, it could be a mounting issue as you want the engine mounted solidly to the frame with no rubber spacers of any kind in between the engine and frame. The more solid and rigid the engine is mounted to the frame the better and most if not all the vibration you're feeling will go away. These engines also tend to have a lot of vibration when new and it'll go away as the engine breaks in as well.

Here's a good thread for you.

http://motorbicycling.com/showthread.php?t=57383&highlight=knife

You got the right idea on the 1/2" thing, the idea is to give a very smooth transition to the port so more air can move in or out... I do most my work with the dremel but switch to a flat file to straighten things up and finish with fine sandpaper. Same applies for the transfer openings. When I say 1/2" tho, it's a rough estimate, but 3/8" to 1/2" would be a good tolerance here. For widening the ports I'm talking about the sides and not the roof or floor. Raising the exhaust roof by 1mm is beneficial tho, then ramping a piston to see how much further you can go before you lose power or until you feel that "happy medium", measure how far down you ramped, then cut that amount out of the exhaust roof and put a stock un cut piston back in. The only way to increase transfer duration tho without effecting the blowdown would be to ramp the piston so my newest engine has transfer ramps but no exhaust ramp.
I think you got the idea of knife edging so no need to explain there...
And for the engine mounting, take the inner tube sections out and just mount it nice and tight, take it for a ride and you should feel the difference... even the slightest movement on the mounting is enough to give the engine that "running start" to hit the frame and over time it can cut thru frame tubes... There's a lot of discussion on this in here as well.
For the exhaust, you're right, these X pipe headers are a waste of time and money unless you just like the way they look, they're just too short to make any real difference, but may come in handy if making a custom exhaust setup, but that's about it. If you really want a good custom pipe and money's not a problem you could get an expansion chamber from Treatland and weld it to Fred's Fire Breather header or use his Kx fire breather adapter, this is one of the best exhaust headers out there for making a custom setup. Otherwise, the SBP pipe works great. I made my first pipe out of a KTM 50 pipe that was cut up and the bends re clocked until it fit, but my new builds are getting kx 65 pipes. Even on the 50cc KTM pipe, the stinger is almost 1" diameter so there's no restriction there, and this is one of the bigger factors for top speed. Even with a straight pipe the bike can hit some impressive speeds once the restrictions are gone. As far as modifying pipes go, cutting up pocketbike headers or cutting the bends out of a stock pips end welding into your setup is an easy way to get the bends you need, same with an old set of handlebars, they're good for harvesting bends from and old Harley or other big cruisers wil usually have the 1" bars.