Give us a run-down of your EXACT break in process. It makes all the difference in the world. Did you prep your piston? Chamfer your ports on the cylinder? Relieve the exhaust bridge? Drill oiling holes in the piston?
Another HUGE mistake you made was riding the ody without doing a plug chop. You could still have been lean on the jetting and would never have known it. The spitting and sputtering on top end would/could indicate a lean condition, starving for fuel, coughing, etc...
Here is what your build and break-in process should be...
1) Bore/hone cylinder within allowed clearance to new piston
2) Chamfer all ports to remove sharp edges as well as relieve exhaust bridge
3) Drill 3 oiling holes in piston per weisco instructions
4) Prep piston by removing all sharp edges around crown, skirt, and anywhere else
5) Flush out lower end with premixed fuel, fill lower end, slosh it around, dump it, repeat as needed
6) Assemble
Engine with 1 base gasket, if you want to lower compression use 2 full head gaskets (although you shouldn't need to, unless the head has been decked)
7) I would suggest putting in a larger main jet BEFORE starting Engine (being fat is a better starting point than being lean)
8) Start Engine and let it IDLE for 10 minutes with a fan or two pointing at the Engine
9) Allow Engine to completely cool down and re-torque base nuts and head nuts
10) Start Engine and let it IDLE for another 10 minutes with fans for cooling
11) Re-torque nuts after Engine is cool
12) Time to ride. Ride it for no more than 10 minutes, NOTHING OVER HALF THROTTLE!!! Also be sure to vary your throttle position, burp the gas, if you hit a lean spot and hold the throttle in a fixed spot you can blow it up. After 10 minutes, SHUT IT DOWN AND LET IT COOL.
13) Repeat step 12 after Engine has cooled.
14) Repeat step 12, but now step it up to 3/4 throttle. Be sure to let it cool completely between runs.
15) Repeat step 14.
16) You can now do a few plug chops. Once your jetting is close, AGAIN, I SUGGEST RUNNING IT FAT and carry a few extra plugs, much easier to change a fouled plug than another Engine build.
17) You can ride the odyssey at this point, but the first full tank should be ran at an easy pace, do not just hammer on it.
If you follow these steps, you will save yourself from having to swap to a 4 stroke and your Engine will last you a very long time. You should start with a 480 to 500 main jet. I had the exact setup you have and I was lean with a 480 main jet at 700' elevation. Also, since your Engine is still air cooled, DO NOT simply shut the Engine down after a hard ride. Also, do not come to a stop and let it idle after a long hard ride. You need to keep air flowing through those fins. Cruise it around and let the Engine gradually cool down. If you cant afford a water cooled setup, add some fans. Also, I noticed you said your brother was riding it when it blew up. I would highly suggest that your are the one to ride it while it is breaking in as well as you be the one to put the first full tank on it. That way, you know for sure what is going on with it.
Take your time and good luck.