Hi Eddy, yes I would drill the other 2 neck screw holes, take the neck plate out and make sure all 4 holes align, they should do if you can see where the 2 hidden/filled holes are.
These veneers are usually thin so don't sand the back much more. If it was my kit I'd probably get a darker colour timbermate and go over it again to hide the pink. For best grain popping effect go for ebony colour Timbermate is the darkest. Will suit the gold stain better than pink !
Wow the mahogany TM I'm surprised came out so pink