I'm an old "R" guy, so excuse me if I speak out of line with some particulars.
First off, sorry about your luck with the farm bike. I've had the pleasure of working on a number of them and most of them I was wishing the owner's didn't work on them at all.
You'll be chasing all kinds of different symptoms if the bike isn't mechanically sound. Meaning that the parts that are supposed to be there are, and that they are functioning properly. Seems obvious, but chasing ghosts are common when you start to get frustrated.
I sorta skimmed through the last 3 pages, so if this has been suggested, I apologize. With that said, you'll be chasing jetting issues till your ready to light the bike on fire if the hot start isn't working properly. The hot start cable, plunger, and carb orifice need to be spotless, and operating properly.
You're compression numbers are a bit off. Manual for my R says 64psi. It shouldn't vary much. Do the test consistently, do not introduce variables in test procedure. Be sure to open the throttle fully while kicking. 50 is low...
Your valvetrain sound like it's bad. In general, farm bikes don't get properly maintained, especially the air filter. Dirt is the mother of all valvetrain evil on these bikes. I'm betting when you got it the air filter resembled a perfectly cooked fire-roasted marshmellow?
Timing needs to be spot on. If you're doubting it, it might be off. Try using the ignition side peephole. It has less parallax. Line up to the second hash mark on the flywheel. Grab a non-frustrated friend to double check you.
TIP: Take a systematic approach. Don't work on different areas all at once. Approach each system separately. Ensure all the correct parts are there, that they are correct, and functioning the way they should. Many times, we loose this once we start getting frustrated.
Do you have a Honda service manual? if not, you need one. My experience is that they are the best in the biz...link:
http://www.helminc.com/helm/product2.as ... itemtype=N