I would check a couple of things. First, remove the kill switch wire from the circuit and run the bike. (Pull choke to kill or put in gear with brakes on) The wiring or switch might have been damaged in the truck.
I would air test the motor. If the RH crankseal is leaking, it will draw in oil from the tranny under load. This will cause extra smoke that isn't normal. Block the intake and exhaust. Replace the spark plug with a fitting from a compression tester with the valve removed. Attach a hose to a low pressure gauge and hand pump. Pump to 8-10psi and shut off the air. The motor should hold pressure. If not, track down the leak and repair. Common areas for leaks are the crankshaft seals, but a 2-stroke can leak at any gasket or even where the case halves meet.
When you had the top end off I'm sure you checked the reeds. If not, check them for wear or damage.
It wouldn't hurt to pull the muffler and try it. Sometimes a bike will flood laying on its side and the gas will gum things up as it blows back through the exhaust. If it runs worse, that would be an indication it's too lean. If it runs better, that would indicate it's too rich.
I would suspect float damage but you mentioned you looked at this. I would double check the float valve and replace if there are any signs of wear. On a bike that old, it should be replaced anyhow. I would also check the needle in the slide. The needle itself can wear where the clip attaches and cause problems.
Last up would be the ignition. It's possible for electrical parts to break down at higher RPMs. If you have another coil, I would swap it out. The CDI is hard to test, but about a year ago I found a site where a guy made his own KDX CDI box. It's fascinating stuff and the tests and mods he did, might help you out. Go to http://www.geocities.com/a57ngel/moto/CDI.html
Let me know what of that you have checked and get back to me if you can check the rest. We'll work forward from there.