Yamaha have been making electric start XT600 for about 20 years, so as you can imagine there have been a few changes. Not so much the engine itself, more things like oil-coolers, oil pipes, clutch arm/cable, wires, oil in frame or in tank ect.
The engines will swop from frame to frame (I've seen XT600e in Tenere frames) as all mounting points are pretty much the same.
Some have clutch-arm on left (3AJ), yours will have it on right side, so slightly different bottom end. Heads are pretty much the same, though early kick/electic starters had decompressor (can be removed).
I'm not sure about gearbox ratios.
Just have a good look at 'spare' engine, checking wireing conectors.
Nothing too difficult to sort out.
rust & dust