"Am I tuning these too low at 12.5hz? What do you recommend?"
that is a personal preference. some folks can't really detect anything below about 15hz +/-. if you have lossy wood floors, the vibration lower than that may be an effect that you can enjoy a little.
the lower the tune, the more excursion the driver makes, which you can see on the excursion tab. the uxl has pretty big excursion, so 13hz or so would still keep the driver under control at full power. tuning a little higher gives a little more spl a little higher up in frequency where it may matter a little bit more. he other factor is build simplicity. I haven't checked but with something like the martysub, a single slot can tune it to about 15hz or so, iirc, lower then that and it has to bend and go up the back wall. no biggie, just something to be aware of. anything from 12hz-17hz should be fine.
" How close to a wall can I place a vent in a box enclosure. In my example, those ports would be 27 inches in a 28.5 inch space. That seems real close."
for a port, best to leave at least one port height to a boundary. if using a 6" port, 6". if using a 3" tall slot, at least 3". jamming it up can mimic a little longer port, but best not to get too deep into that.
" Should I flare the intake or output side of the vents?"
ideally yes. some empirical data here: http://www.subwoofer-builder.com/port-flares.htm
something like the martysub does ok without roundovers/flares though.
"Which would be better - one 6 inch or two 4 inch ports? I thought the two 4 inchers would have lower air port velocity, but it appears the same as the single 6 inch port."
best to use fewer ports and larger ports. 8" is probably the minimum for the uxl at full power in a low tuned cab. check air velocity at full power (2200 watts or so).
"Does it matter which direction I face the driver or ports in the box enclosure? Can I turn a side-firing driver directly at a wall so we just see the finished sides?"
that is fine. doesn't impact performance.
"Can I put bends in the ports to get longer ports in smaller boxes? I have seen this mentioned before, but all that is said is that "it gets complicated" with no further explanation."
yes. bends do many things from reduce pipe resonance effects to turbulence to effectively lower tuning. all these effects are not well documented, which is why folks say "complicated" with no further details. member neo dan has a sub with multiple bends and measured results. easy button end table i believe was the name of his threads. there were several versions. if you really want to dig into it, have a search on that. i don't recall the links off hand.
"I have read that we all want the smallest enclosure with the lowest possible tune. But it is all about compromises. This is my first stab at designing something decently-sized with a low tune for movie viewing. Do you have any other ported suggestions for a smaller ported, low-tuned enclosure?"
the smaller the internal volume, the longer the port has to be. the lower the tuning frequency, the longer the port has to be. the larger the diameter of the port, the longer the port has to be. all these effects make it impractical to build a small, good performance, low tuned sub, which is why you don't see them.
"Since aesthetics are important to my wife, do you have suggestions for a sealed enclosure? What performance do I lose if I go with smaller sealed enclosures."
a comparison in winisd can be made or there is also a comparison of sealed vs. ported in the martysub link. the amount of spl given up is in the ballpark of 10-12db around the tuning frequency, which is quite a bit.
" Sorry my questions are all over the board. This is all new to me."
excellent homework. excellent questions. excellent post!