Well, a bit more progress. I was able to test-fit the engine/transmission/headers in the vehicle this weekend. It was definitely a good idea to pull the suspension, mount the engine/trans/headers to the suspension and then lower the Cuda down onto the suspension. The test-fit and clearance process took around 10 fittings. (lower Cuda until something touches, mark the contact point, rase the Cuda, use a BFH to make some room, repeat as necessary). I did this using a gantry crane and hoist.
For the record, I'm using a 6.1L engine, TTI headers, RMS AlterKation front suspension, and a 4L60E transmission. I have to say that the transmission mated up flawlessly. I purchased my trans and the necessary adapters from Phoenix Transmissions. Excellent service and customer support.
This combination required the making room in the trans tunnel on the passenger side for the transmission. Specifically, room for the transmission lines so that the lines could be installed, room for the lower portion on the trans on the passenger side for what I believe is the access to the gear pack(??), and the pinch seam in the area of the bell housing. I also needed to flatten a bit of the large humps on the engine side of the passenger A-Frame support. (So where the upper A-frame bolts to the body, the actual bulges on the engine side). Also, I had to cut about 1/2" from the flange of the transmission bell housing that is used for the dust cover on the passenger side so that the headers would clear the transmission.
The car is now at the body shop to get the undercarriage, interior, and engine bay painted... then back to me for engine/trans/suspension install.