Update: Front almost completely sanded back, plugged the holes with a larger patch which of course chipped out when drilling the new holes!!! At least I'm getting good experience at patching holes.. will now need to see if I can get the colour to hide the patches.
I had to put it together just to see what it would look like and make sure I got the alignment correct this time. String height was a little high, but I'm hoping I can bring that down with sanding the nut lower and tightening the truss rod (fair amount of bow from the string tension), otherwise I'll have to grind the bridge which will be an experiment.
Intonation was actually pretty close, so that's finally a positive!