Just an update on this project.
Firstly, Intercooler part 5170704AJ is indeed still the thicker unit, so I'm good there.
The truck is back together and finally running again. The BD turbo came with a new downpipe which is about 4 feet long. This required dropping the transmission x-member and also completely re-plumbing the stock exhaust as the new downpipe terminated right smack dab in the middle of the catalytic converter!
I also torqued down the intake elbow too much and cracked it, so now I have a new BD unit there too.
I'm taking it easy on the turbo right now, but ran it over the weekend and it makes good boost and no oil leaks so everything appears good to go. Thanks for all the advice on this thread and other older threads too. This community is such a great resource!