No worries Willem, have a crack using the dremel with a small router bit, only take off small amounts and check the pup fit. If you still need help I'm happy to help on a weekend, I'm in Willetton.
With regards the glue I don't think it will be an issue with solid paint. Once the body is grain filled and sanded to 320 or 400 grit see how the first coat of primer goes and if it does react with the primer you will need a small wire brush to remove the glue.
Best of luck.
I'd get the pups cavities routed first, pups fit snug then please post me the nut to 12th fret and 12th fret to bridge distances, I ended up cutting a slot south of the 22nd fret with a bandsaw right at the end of the build when I realised ! Was I nervous !
The gaps in the neck pocket will most likely be filled with glue when you set the neck so I wouldn't worry too much about that