Would it be advisable to get a 6 point harness with stock seats? According to the FIA, the shoulder straps have to rest on the seat flat, which the Z seats aren't designed for. Obviously, this includes a roll cage, don't worry. But, I would like to maximize my safety, hence the harness and cage. Would it be safe to mount a 6 point harness onto the stock seats? Could I just mount the anchor points right behind the seat, reducing the chance that they will even be resting on the seat? My other option is braum leather seats, that match pretty closely to the stock leather seats, both in color and style. Thank you!

If you need 6 point restraint and a roll bar you also need a proper seat, something with bolsters to keep you in place. The stocks are a one person bench.

Absolutely not. The seats need pass-throughs that capture the sub and shoulder belts. Otherwise, your harness will not function as intended and you're going to have a bad time. 

I'm assuming (hoping) this is a race car that doesn't see the street. A roll cage and race harnesses are not fun nor safe on the street (unless you're wearing a helmet and HANS device at all times).