wow! that was a tough read there.
First the jetting is way off on the bike. That is why you have a lot of carbon in the cylinder and exhaust. You will need to clean up the pipe and everything while you have it down. Here is the jetting specs to clean the bike up:
Slide = #6
Needle = Kehin CCH, 2nd or 3rd notch from top
Main = 158-162
Pilot = 40
The bike is jetted way off to start with. That will lean out the car and bring it close to the KX specs of the year. It is what I am running and ran out in Milican (open desert, LOTS of sand) last weekend flat out for 70 miles without a hickup.
You will want to get a complete gasket kit for the bike. Cost will be about $35. You can get one off ebay from K&S performance for the 88-92 KX250 with all the seals you need. It will also come with a KX headgasket that is thinner than the stock increasing the compression and performance.
For the cylinder, there are different sized pistons out there. Something like A-D. I am going to have to tackle the same thing this winter. Take the cylinder down to a shop and have them measure the unit and go from there.
For the Boysen reeds, you will need to contact them directly for replacement parts. You may want to consider selling that unit like on Ebay and getting the V ForceII cage. Seems to be a much better setup.