Thanks, Karl. I figured most of that stuff out but it was being problematic because the autodetected markers from the drums were not lining up with the ones from the other tracks. What I'm doing now is manually inserting markers at each measure using snap across all tracks following the tempo map I created. Then I'm going to try creating a new, more in time tempo map and using those user defined markers to drag things into place to get the overall project in the ballpark. I'm concerned about phase relationships but I don't see why this shouldn't work. I'll use the merge and lock/double click/pool stuff while making more finite corrections. However there are some things that need to be separated in the drums for correct (if a kick doesn't match a cymbal crash for example I'd want to move those into place independently) so that may cause phase issues. My solution though is to gate stuff to hopefully get rid of any unnecessary bleed that would contribute to that. There will likely be some sample helper tracks for the drums as well so that should hopefully mask any issues further.
This is indeed a grand undertaking. Might as well jump in with both feet at this point, eh?
Thanks again.