The port timing acts the same way cam timing acts in a 4 stroke engine, of course, we don't have cams and in order to change the timing we need to cut at our ports, especially on the exhaust roof and intake floor, this is how we control intake and exhaust duration. Widening the ports has the same effect as having higher lift on a 4 stroke cam, however, it's the duration that has the most effect on an engine's performance and at what rpm range the engine's powere band will be in. This is the rpm range where the volumetric efficiency can exceed 100%, meaning at a certain rpm or rpm range, the engine is actually taking in more air than it's displacement like let's say our 66cc engines would be pulling in 75cc's of air fuel mix on each intake stroke, figuratively speaking.
Now we can't get all this extra power for free, if we add more to the top end, we lose some at the bottom, and if we add more to the bottom end, the top end suffers. It does pay off tho to add more to the top end and gear the bike lower, or add to the bottom end and gear higher. We can also recover some of this lost power by increasing our compression ratio, but there's also a limit to how much we can do this as well, and in some cases, increasing the compression ratio can even cause a performance decrease.
Increasing the exhaust duration has the biggest effect on top end rpm, but also top end power to a certain extent. Adding too much exhaust duration also effects the blowdown, or how many degrees the engine is producing power before the exhaust port opens so also keep this in mind when opening the exhaust port roof.
On the itake side, we lower the floor or cut out part of the bottom of the piston skirt, or cut holes into the piston in order to increase intake duration. We have limits here too.. especially on the piston ported engines as the duration increases past 90 degrees, the piston is actually pushing the air/fuel charge back into the intake manifold, and the carb at lower rpm's, but at higher rpm's where the air is moving toward the intake faster than it can be pushed back out, we can see a gain at a higher rpm. At higher intake durations, we lose idle quality and low end power due to this blowback, but we can usually run up to about 110 to 115 degrees intake duration with decent results and keeping the power at a usable rpm range.
With a reed valve, we can go considerably higher with intake duration because the reed prevents this blowback, and the power is much more noticeable in the lower to mid range with the power tapering down to about the same levels as a piston port at the higher rpms.
There is one other method of controlling the intake while preventing blowback, which is the rotary valve, this is basically a disc that spins with the crank and has an opening in it to allow air in only at a certain crank position and it's closed of during most of the down stroke, this configuration does make the most power, but at a much narrower range than reed valves or piston ports. Rotary disc valves are typically on the side of the case and need the carb to be mounted on the side of the case as well, but some engines will have the valve behind the cylinder and spinning off a bevel gear on the crank, but in it's simplest form, you'll usually see the carb mounted to the side of the case. You can run up to around 200+ degrees intake duration with this setup, but the engine won't be as strong at the bottom end or midrange, then it hits Hard once it comes up to it's narrow powerband. Great for road racing where the engine speed is pretty much constant and running in a very narrow rpm range.
I'm not going to recommend you any timing specs to follow because every engine is different and there are too many variations in gearing, tire size, bike weight, rider weight, outside temperature, and elevation... Basically, what works for me may not work for you or someone else. Read the 2 stroke Tuner's guide by Gordon Jennings, and also Graham Bell's 2 stroke tuning book to get a good idea of what all is going on when you rais the exhaust roof or lower the intake floor, or even widen a port etc.
Start by cutting a small amount at a time, this requires taking the jug off and putting it back on several times, but it'll be worth it when you hit that sweet spot.
Start by indexing the piston, cutting off about 1mm at the exhaust port, and 1mm at the transfer openings on the piston crown and about 5mm from the bottom of the skirt at the intake port. Use a degree wheel and record all your opening times so you can refer to them later. Once you got a good port timing by indexing the piston, you can map out the ports on the cylinder and cut out the intake and exhaust ports accordingly.
An easy way to see what you're doing is to remove the piston rings and coat the inside of the jug with Dykem, a dark blue dye for machinists, this stuff stays put pretty well, but you can scratch scribe lines and be able to see these lines really easily. Once you paint around your ports with the Dykem, you can assemble the engine with a NEW UN CUT piston without the rings on the piston (the rings can scrape off the dykem so that's why they're removed for this step) Install the base gasket or gaskets you'll be using, put spacers on the cylinder studs (we're not installing the head so we need spacers so you can torque the jug down)and torque the nuts down. Now connect a protractor or degree wheel to the crank and find a good reference point like the rear corner of the mag cover or make a pointer out of a piece of wire. Bring the piston to TDC, set your degree wheel so the pointer is pointing at zero, or rotate the wheel so zero is lined up with a good reference point and tighten up the degree wheel enough so it won't slip. Remember those numbers you recorded when you cut on your piston? We need them now. Turn your crank to the same degrees you wrote down for the exhaust cut on the piston and mark this on the inside of the jug with a scribe using the new piston as your ruler. Now rotate the crank to where the transfers were working their best and mark a scribe line here above the transfer ports. Once you got the lines scribed in (you could use a sharpie with no Dykem, but the sharpie marks may wipe off when you least expect, and the sharpie is no where near as accurate as a scribe line when dealing with fractions of a milimeter) now it's time to disassemble and remove the jug. Cut out everything under the scribe lines and chamfer all edges to prevent ring snags. Use a pencil grinder if you got one, a dremel with a flex shaft is second best, but pencil grinders are under $20 at Harbor Freight, but need a 30 gallon compressor minimum. Use carbide rotary files to do the big cuts, then switch to diamond coated burrs for the more precise work, sanding rolls and drums work really well too, but the diamond coated burrs are the most precise. Run the grinder rpm as fast as it'll run nad use a very light touch, don't try to force the cut and let the tool do the work. Remember the pencil grinder? these guys spin at 54000 rpm so they can cut pretty fast, even with a fine diamond burr just by barely touching the work piece, they cut fast, but very controlable at the same time... I can't recommend the daimond burr set enough when it comes to precise work. The pencil grinder will also reach into those transfer openings you'll never get close to with a dremel too.
Once you got all your ports cut out, go back to the intake port and rough up the inside with a 100 grit sanding drum, just get that smooth sanded texture, that's planty good enough to disrupt the flow and create the turbulance to keep the fuel well atomized.
You can do the same up the transfer openings going up from the bottom if you wish.
Go back to the exhaust port and sand it with the same 100 grit drum, then switch to a kratex cone and polish it out. Kratex is that fine grit impregnated rubber polishing cones that come in some of the dremel polishing kits, this'll leave an almost mirror smooth texture so the exhaust can flow out slightly better and carbon deposits can't stick to the nside of the port.
Once you're ported and polished AND happy with your work, go back in and chamfer all your port openings with a diamond burr, needle files, or fine sandpaper to take the edges down, this is very important or all your work can go down the drain in a matter of minutes by either snagging the ring or the nikasil can start peeling off. A good smooth chamfer will prevent this.
Sorry for being long winded but there's just so much to porting and changing your intake and exhaust durations that it's difficult to explain quickly and simply... hope this all helps someone.