I'm replying here instead of PM so that I can be corrected if wrong. Also it may answer questions non posters may have.
The 93-98 Lincoln MK VIII engine is basically the same as the 96-98 Mustang Cobra engine. That's where the Cobra got it's engine from. The differences in the engines are the exhaust cams (fuzz different for smoother idle in Lincoln, no power loss), the intake design and the forged crank used in the Cobra. The reason for the power difference is the intake manifold and the exhaust manifolds. The intake for the MK VIII was designed for torque on the bottom end for the automatic transmission while the intake for the Cobra was designed for higher RPM use with a manual transmission. The exhaust manifolds on the Lincoln have the converters mounted right up on the passenger side and the converter is part of the drivers side manifold. That kills top end dramatically which hurt the HP rating. But it makes the car quieter and lights off the converters faster for better emissions. Plus, there really isn't that much room under a MK VIII. It's weird, the car is huge but almost every available space is occupied by something.
http://www.kennebell.net/superchargers/ford/mustang-cobra46/mustangcobra46.htm
The Kenne Bell website can answer the supercharger questions better than I can.
The truly weak point on the Lincoln motor is the same as on the Cobra motor, ring package too high on piston. Cast or forged crank is of no importance on these street pieces except for bench racing points. Next weak point would be the rods.
Also, since the KB unit is not intercooled and the inlet path is convoluted, you can't make as much power as with a newer motor. You never stated which car you're using but the Lincoln uses vacuum controlled IMRCs while the Cobra uses electrically controlled IMRCs. You'll need to use the Cobra control with a window switch. Lonnie can give you more info, he's usually on TCCOA forums.
For fuel, 255L pump in the tank, 42# injectors and a Cobra air inlet/filter assembly. Computer must be chipped, SCT is what I'm using. Tranny should be rebuilt to 'Jerry' specs and running a cooler. Radiator is OK stock but should be upgraded if you plan on actually using the supercharger. (There are a lot of show cars out there, you know the ones).
I can't think of anything else offhand. I'm sure I've missed some stuff. My KB unit is still collecting dust in the basement. I've upgraded the brakes, chassis, computer and some other junk but keep procrastinating on the blower.