How to fix miss.firing

Hello, i went thru a nicotine withdraw and with bad concentration made a really stupid mistake. I am very embarrassed about it…(especially because i am an Mechanical engeneer by education…)

I have recently rebuild the YAMAHA XJ500 1981 (bassically a rare European version of XJ550, seca, etc.), picture bellow:

The rebuild took time, my battery died (before rebuild and during it motocycle ran like a dream).

I connected electricity to start it up from a running car and without battery in the motorcycle…it didn’t start, then i connected cables from a car backwards (switched +/-)to the motorcycle (still without the battery on the motorcycle)…
BEFORE I REALISED WHAT I HAVE DONE, IT WAS TOO LATE..

I then changed regulator, ignition coils, CDI , FUSES all 5, starter relay solanoid.
now it cranks up, has spark but will not run or start. If a crank it for a really long time it fires on a cilinder or two, wont rev and then dies. I suspect missfiring?!

I tried to find solution for 2 months now..but couldn’t
IF SOMEBODY HAD THE SAME ISSUE PLEASE HELP ME, I AM DESPERATE…(and extremely embarrassed)