It really depends on what you want your cars main use for. It sounds more like a driver, so I wouldn't concentrate too much on 1/4 mile stuff either.
I have a '69 Mach with 3.89 gears and 28" tires also, but no overdrive like you have. 3.89 is as big as I want to go with my 4spd so that I'm not winding the engine out on a highway. That puts me at about 2800-2900 rpms @60mph. With your overdrive, that would put you about 2300 @60mph. 4.11s would put you at a little over 2400. 4.30s at 2540. Still pretty reasonable. I would definitely step up to either 4.11s or 4.30s depending on where you want to hold your highway cruise RPMs at. It would really make a big difference with either.
As for the rear choice, the later Detroit Lockers that I have used have no "clunkiness" to them. The old styles were somewhat notorious for that when going around turns, and a lot of guys can't get that impression out of their minds. I just haven't seen it with the newer Lockers. I love them and wouldn't use anything else for a solid performance car. They're bullet proof, trouble free, NO clutches to wear out or hassle with. They're basically a lifetime trouble free investment for anything short of a drag car. The only drawback is having to watch any sudden throttle gooses around corners, which usually isn't a good idea on any car unless you like getting friendly with curbs and parked cars.
The 31 spline axles and N case or similar stronger aftermarket case is also a wise choice.