Sometimes using the input shaft spline from the gearbox can work as an aligning tool - even if it is a bit of a pain to move the gearbox around into place.
As far as clutch prep and flyhweel cleaning goes you could probably use acetone if you got it handy - brake cleaner would also work (seeing as they are both made for the same purpose, using similar materials i think).
It might pay to check if your flywheel is warped as well.
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