You may have had a faulty R/R that was failing slowly enough to cause some wire melting before blowing the fuse. The repeated attempts may have caused some more melting.
Anyway, at this point I suggest getting a good multimeter and testing the main electrical components (stator, R/R, coils, etc.) to verify that they're all up to spec (see stator papers in the garage section of this site). You will be a bit intimidated at first but once you find the problem you'll say "Got ya!" and you'll feel better about not having to play guessing games anymore. When I found my R/R putting out 18 volts, that sure clarified the problem.
If all of that checks out OK then check to verify that all plugs are firing (see other posts on how to do this). I'd also try to pinpoint exactly which wires have melted so far, if I were you. It would be a shame to get everything else straightened out and then have short circuits that will mess you up again.
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