well I put back everything and decided to ride it 10 miles. It is running great here is a video link - hope it works: https://vimeo.com/manage/videos/1100882325 however I have to drive it in 2nd gear. I only putzed around 10 miles in my neighborhood. It did not really want to go into 1st - mostly started in 2nd - could eventually get into 3rd and 4th not 5th - would go back into neutral and neutral light works -false neutral in between 2nd and 3rd -
The false-neutral situation, along with the balky 1st-gear selection, suggests a bent "L" shifter fork. You'll only be able to determine that, though, by pulling the engine, removing the transmission, clutch, and alternator side covers, the shifter arm, then those [same] selector indexing parts, the 4 screws that hold the countershaft bearing in the lower case (and pull that out) and then separate the cases. You can then shift the gears in the lower case by turning the shift drum: watch the 2 gears nearest where you removed that countershaft bearing. If it shifts the most-outside gear (C5) deeply into the next gear toward the engine's center (C2) for 1st gear, but barely engages the C5 gear for 2nd, that is the typical bent-fork scenario. This happens when the bike falls over to the left side and the shifter hits something solid while the engine is not turning: the weight of the bike on the non-engaging C5 gear bends the tines of the "L" shift fork. There might also be evidence such as scrapes on the grooves of the C5 gear or on the sides of the "L" shift fork. (The "L" is cast on the side of the fork, but not visible when the fork is mounted to its slider shaft: the gears are in the way). Sometimes (pretty rarely) the sides of the groove on the C5 gear are burred up or burnt-looking, too, helping you to identify it.
Most of these that I have repaired got bent when the bike fell over in the owner's garage and the shifter hit something solid, like a brick or paint can, stored next to the bike. It tried to shift into 2nd with the weight of the bike on the shifter! That's a LOT of force.