Only the 2nd Gen LS ('03-'06) uses CAN. The 1st Gen LSes are OBD-II.1) Engine management - the LS is a "canbus" style car -- all of the components of the electricals talk to eachother via a bus.
The adjustable pedals are only available on the 2nd Gen LSes, and then they're only optional. (My' '04 had them; my '06 doesn't). The manual tranny was only available on the 1st Gen LS V6, so the adjustable pedals aren't an issue.2) Pedals - the Lincoln, IIRC, has Ford's electric movable pedals. I don't know what the manual car had. You will have to either retrofit the manual pedal box (which may or may not even work), or go full custom pedal box, which is more expensive (maybe not! 5spd Lincolns were rare), but could be easier.
It uses a Jag 8" punkin. As you said, if you're going to the trouble of switching to a Mod Motor, the work to adapt a Mark VIII/Cobra punkin should be trivial.3) Rear-end - the LS uses a weird rear end.