I have both, carry both regularly. They are both really nice, though mine are heavily modded so not exactly apples to apples. I also shoot hotter ammo than most on a regular basis. My 43X is comp'ed while the 48 is not. 48 seems to have a smoother recoil impulse even with the 43X being comp'ed, but I enjoy shooting both. Both feel great and I'd say I shoot them equivalently, unfortunately I haven't been able to take them out to 150 yards yet (yeah, 150 yards). Time will tell if they can do as well as some of my other 9mm guns do.
I do use the Shield mags and so far haven't had a problem. I've seen where the early gens did have some issues, but I carry the 15-round in the gun and the 15+5 (20 rounds) as a backup.
I don't think you'll go wrong with either. If they both feel good to you, I'd base the decision on how you plan to carry. I don't carry IWB so the barrel/slide length is less important to me. With OWB carry, my cover shirts are long enough to cover the extra little bit of barrel/slide length.
Oh, I should also add, I would ABSOLUTELY spend the extra few bucks and get the MOS version even if you don't plan on putting optics on because the MOS version has the railed frame. I've only see the railed frames on the optics and the TLR-7Sub SMOKES the TLR-6. I hate the TLR-6 light, but one of my guns wasn't an MOS and I'm stuck with that crappy light for a time now.
Haywire is right, HO is a great resource, but as always, YMMV.