Hi Legendstratocaster555. Firstly I find tremelo's a pain at the best of times (Exception, Bigsby) If you don't use a tremelo much.? I would scrap the idea. However, thats your choice, you can mill it but I would check with an engineer how much to remove as there is a lot of tension on the neck.
Ref bridge position...Measure from the nut (Fretboard side) to the top/middle of the 12th fret. Whatever that measurment is, lets say its 12 1/2" Then from the top/middle of the 12th fret 12 1/2" is where the string should cross the bridge saddle, This is where it should be located.
With regard to thickening your axe nothing prevents you glueing another piece of timber on the rear side (My choice). Make sure you don't get a heavy timber as it can give you physical aches and pains if the guitar is too heavy.
Regards Fenderphil
Would you take advise from this man.? Just joking.