The differences between a Lincoln 3.9 and one of the supercharged Jag engines is very much the equivalent to the differences between 289 Ford and Boss 302 engines. Neither swap is as simple as changing a radiator cap, but both are very fully do-able.
Physically, and aside from the possibility of hood interference, the greatest difference is in the location of the oil filter---the Jag has it on the passenger side of the engine and the Lincoln has the filter in the front. Fixing this is a simple matter of swapping hardware.
The supercharged Jag engine has no VVT. If swapping the Jag into a first design Lincoln, that works out well since the Lincoln doesn't have VVT either. If your Lincoln is the second design, you'll have to work with the folk at SCT, who assure me that they can handle the alteration of turning off the VVT controls.
Match the sensors on the Jag engine to the ECU in the Lincoln. The wiring harness on the Jag engine is of the same design as the one in the Lincoln, and one physically plugs into the other, but it'll be necessary to trace the individual conductors and perhaps move the connections inside the connection point to achieve a match-up.
Some time ago, I googled until I found a business whose main activity was scrapping Jag stuff. As I remember, they had several examples of blown Jag engines and were selling them for $3K to about $6K. Add in a grand for peripherals and have a blown Jag engine in your LS. Or work out a deal with Quik to acquire some of the hardware he has developed. Or go on the internet and get one of the generic turbo kits.
Or do the job yourself. I refer you to 'Land Speed LS', even though it's going almighty slow due to the necessity of paying attention to more immediate things!
A personal observation:
Over the past several years, I've noticed the changing of the make-up of the people on the LS portion of this forum. I bought my LS new and paid something close to forty grand for it. Very many of the newer members here seem to be kids who paid five grand for a car with a hundred K miles on it and their modifications start---and often end---with a hundred pounds of sound equipment.
When I was in high school, it took me an entire weekend to change the intake manifold on the family car. That would be a couple hours job now. Don't bite off more than you can chew. And the fact that the intricacies of an engine swap may be beyond your own level of experience doesn't mean it can't be done.
KS
Sorry for the soapbox---at least a little bit---and also for my part in high-jacking this thread. The 302 swap can surely be done!