Spent a few hours carefully finding and drilling all the holes. Basically, find the hole, re check it a few times, drill it, then re check alignments of strings. I used so sewing thread as that was the closest thing to twine I had laying around.
So a checklist of what I did :
Neck Screws, Tuner screws, Pickguard, Pickups, Knob/slider plate, Tremolo.
Once everything was screwed on I installed the E strings to have a quick play (Limited play) for a bit of a reward. Its sounding good! The only holes left to drill are for the input jack, and the strap leads. Input jack will be done after I've removed everything (The cables are forced out of the hole at the moment so they wouldnt interfere with the internals whilst drilling the other parts).
Now I get to remove everything, finalize the sanding and then it is ready for Staining.