Hi guys. First time bike builder, but over 20 yrs exp on automotive. I took on a 2000 ls650 salvage project to keep me occupied while going thru chemo and radiation for throat cancer. Paid $400 for it wrecked. It was her sons who laid it over very hard years ago. Put new flywheel, magneto, engine cover, badically all new drivers side engine. I believe the problem may be with the after market timimg module. I set it to tdc. And have .004 lash on intake and exhaust valves. So i dont thinnk it jumped time. And compression is good.
Black and white wires maybe not properly paired with orange and green?
Im stressing because i completly rebuilt the bike before getting to start it. I mean frame off and stripped and painted copper anf white. Looks bad ass. Have pix to send if you guys want.

Ive hit it with enough ether to start, and at first had some spit and sputter. That was while i jad the carb pulled off to rebuild, and just went straight through intake. Maybe a oil clogged exhaust. I saturated with wd40 and oil.

After market module? are you sure it was for the Savage? I'd test the spark by leaving a plug in the head ,and using a second in the coil wire held against the outside of the motor. You might also want to look at the decompression cable setting , there should be some slack in  it when not activated or the exhaust valves will be held open. JOG is right rotation is CCW (the same way the wheels turn)when setting valves at TDC , Clymer book is wrong. You rebuilt right side ,you might want to recheck the wires coming from the pickup coil ,make sure connector is clean and tight and that the wires that run behind the drive pulley aren't damaged. Pouring a bit of oil in the sparkplug hole may help seal the rings, prevent damage, and help build compression .
    p.s. hope your feeling better!

Bust the header loose