Setting Neck to body

So about 2 years ago i got a b.c. rich bronze warloch neck and bridge and installed it on a custom guitar body. I remember installing the bridge pickup from the warloch and the pickup was sticking up (ihave no pictures at the moment) so i set the adjustable wrap around bridge to sit high so the strings can go over the pick up (i should have screwed it into the body more) but when i installed the neck, it sat slapped to the body so i made shims so it sat at a perfect height so the strings can go over the pick ups and over the neck without having any buzz sound. I did readjustments as the strings were too high but i fixed that years ago. After a few years of playing with it, practice and at shows, the bridge began to bend at the bolts (i will provide pictures). It didnt bother me as i loved the look and the sound but it was pretty hard to bend the strings. I realized this when i picked up my friends knock off fender strat. The strings were bending perfectly and the pickups were giving a nice warm sound (i had installed a neck strat pick up and a bridge bc rich pickup, it sounds clean in my opinion, but my sodered job was a wreck and the feedback i was receiving was very... scratchy and earaching. It only sounded great when i played. So i decided to rewire it and get new pickups for a better sound) and the feedback was exactly what i was looking for. And i realized the neck was sitting on the body really close. I picked up another friends epiphone and realized the same thing and i looked at my custom guitar and wondered if i should fix it and let the pickups go futher into the body so the bridge can be bolted in more so it wont bend at the bolts. So my question is, should the neck be set lower than it is now? I put a quarter for reference to how high it is.