Bad Ass III Saddle Ht. Adjustment

[BassScum]

I have a project bass I'm working on. Wayne Charvel made body (Fender P body). I installed a mighty mite jazz neck. Everything seems to have gone well with that. I then installed a Bad Ass III bridge. My questions are. The action is really low, how high can I extend the saddle screws without affecting sound quality or any other issues? It seems like I have to raise the saddles to high to get the strings off the frets. Also I positioned the bridge at the exact location as the previous bridge that was on it (fender style). To locate the 1st string saddle to 17" from the 12th fret I had to adjust the saddle screw and move the saddle pretty far back on the bridge compressing the spring more than what seems like normal. If I can get the intonation where I need it does it matter how far back I had to move the saddles? Will it affect tone? Or should I drill new holes and move the bridge back further? (Didn't want to do that because I didn't want to expose the previous bridges mounting holes). One other thing when I 1st replaced the neck (w/ the mighty mite) and had the old bridge on,the string action was higher and more adjustable but not with the BAIII. The neck is almost perfectly straight (relieved). Should I adjust the truss rod to raise the action (bowed) or rely on the Bridge adjustments?