It is possible for a KZ750 twin to be 180 out of time, but it can't happen spontaneously, so if it ran ok, and the advancer rotor was not touched, then it can't be 180 out. More likely would be that the timing plate has moved, or a wire is intermittently shorting, or the power wire to the coils is not getting full power, or that the igniter is going bad, or that the pickup wiring is intermittent, or the pickup is failing when hot. There are, unfortunately, many possibilities.
If you had the rotor off since then, it may be on 180 out.
I hate to ask, but is there a chance you ran out of gas? A motor will usually idle slightly higher just before it runs out.
You will need a multimeter to really go through everything.
The left cylinder is #1 when sitting on the bike.
You can probably figure out which one is #2.
You can build a replacement ignitor, which you can also use for coil testing on a bench. It's very cheap and easy to build. The details for the twin is at the bottom of the page.
home.comcast.net/~loudgpz/GPZweb/Ignition/GPZgmHEImod.html