Don't forget that the standard air cooled XT600 engine was also used (to great effect) on a few other Yamaha models such as the SRX600 etc...
I would imagine that it's quite possible to mount the engine quite easily but as stated above it's the pipework, electrics, cable routings, and carbs etc.. that may create a problem.
Personally I 'd stick to finding a decent standard XT engine from the same model you are re-newing. It's likely to be a lot less hassle.
Good luck whatever you decide to do...
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Triumph Bonneville 800 (2004), Yamaha XT600E (1999), Honda XBR500 (1986).
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