As far as I know there are almost no aftermarket parts produced for these cars unless it also fits a Mustang. I haven't seen a fox LTD/Marquis in a junkyard in many moons.
The 4.2 V6 heads have machined pockets for the fuel injectors for the multi port fuel injection they used so they will not work with your CFI. Any 3.8/4.2 head from '88 up will have these pockets.
These cars have the 7.5" rearend, but an 8.8" rearend can be swapped in relatively easily.
Your car has a C5 trans. I believe the 2.3 cars may have received the C3, but the wagon was only available with the 3.8/C5 combo.
You can bolt a later AOD or 4R70W trans to your car as long is it has the SBF bellhousing bolt pattern. The 3.8 has the same bellhousing pattern as the SBF. Getting either to work will require some work. The 4R70W needs something to control it. There are standalone controllers available to do this. The AOD is controlled completely by the TV cable so it would be cheaper to get up and running as long as it is set up properly otherwise it will burn up in short order.
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