mint
My first bass was a cheap squire...they aren't super light. In my opinion, if you cut off the top horn, you will have balance problems.
Neck strength should only suffer if you hack it off all the way down at the neck. Maybe just lop the top off and leave a decent stump? If you attempt a large cutaway in able to access the top frets, then you can expect that neck to weaken without the side bracing the top horn provides. If you're not doing handstands on it and jumping around, you should still be OK. Tuning might be required more often?
I'm most curious about your attempts with the controls...can you explain glue them in place..? Also, if you're gonna move the jack, you're gonna have to either open up a new cavity on the back or move it somewhere else in the existing cavity...I think that you might find it in the way if you leave it anywhere in the existing cavity.
Either way, if you want to attempt a frankenstein job, a used squire is the one to cut on!!