Roll your own. The early CT-200 Trail 90's frames will accept Honda 50/70 motors which means any of the current Chinese clone motors will go into them as well. Later OHC frames will accept these motors with some modifications or adapter kits from www.dratv.com
. Another alternative is to build a pseudo-CT from something like a C50/C70 chassis.
eBay is your friend and like John Cash said about the Cadillac in his song you can "get it once piece at a time."
Obviously such a bike won't have the neat features of the original CT's like the high/low gearbox but in some ways you'll actually end up with a superior bike with things like more displacement, 12v. electrical system and a brand-new motor plus the pride of having built it yourself.