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Short Scale Bass Help

I bought a short scale bass off of ebay as a project a few years ago. It was obvious that it wasn't playable since the electronics were messed up and the bridge was in the wrong place. But I know for certain it is a short scale since it is tiny. I refinished it and it looks great, but now I need to drill holes for the bass, and I don't know where to start since I don't want to mess it up by not having the correct lengths, and messing up the notes on the designated frets (if that makes sense). So if someone has any information on a short scale bass that could help me that would be great. I can provide photos and measurements if needed.
 
Measure from fingerboard edge of the nut to the 12th fret. Use that same measurement from the 12th fret to find the approximate middle of where the bridge adjusts. The tough part is getting the bridge centered sideways so your strings are sitting nice and centered on the fretboard.
 
An inch is indeed a mile - completely unworkable.

Best solution is to start over - put wood in the pickup holes to fill them, then carefully locate the bridge and drill the holes. After you know the bridge is correct, re-rout the holes for the pickups. Have a custom pickguard made to cover the erroneous holes....

OR...as a last step, remove all hardware and the neck, refinish the body, then install the hardware.

Dan Erlewine's book on guitar repair would be a good thing to read before doing any more work on this instrument.
 
hold a piece of paper over the hole and take a pencil and just rub gently over it, it should trace the outline of the hole you routed. Take that to a piece of wood, trace onto the wood, cut it out, sand to fit. putty would work depending on the size of the hole and how pleasing it is to the eyes