The sample rate is automatically determined by the MT if you're using the S/PDIF input. So with the UA5, it will be either 44.1, 48, or 96. The bit depth must be set by you, though--Record Settings/Bits and then choose what you're outputting from the UA5, which will depend on whether you have the ADV switch on the back turned on or not.
So, if you have the UA5 set to 24/48, the MT will record the 48 sample rate for sure, but unless you have 24 bits enabled on the MT it will just truncate to 16, as I understand it.
As for the second question, I think you really only have two options instead of the three you listed:
1)UA5 digi out to the MT--this is the same as the first option in the list, using the UA5's A/D, yes?
2)UA5 analog out the the MT
I would strongly suggest going with option 1, not so much because an unmodded UA5's A/D is necessarily that much better than the MT's A/D (I've never done a direct comparison of just that portion of each, so I don't know), but if you're using the UA5 at all, then I think you are automatically using its A/D, even with analog out. My understanding is that the analog outs have been through an A/D conversion and then a D/A conversion. I don't think you'd want to subject the signal to another A/D conversion in the MT, as I don't think that could improve the signal.