88 had the balance shaft, but I don't see that as being an issue with the way it runs (other than smoother).
I thought the 3.8 went MAF in 91, I know my 89 is MAP (MAS?, I know i don't have a MAF sensor in the zip tube), but either way, as long as they retained all the sensors and accessories from the 90 it should be fine, and just just used the long block.
My 89 with the 3.8 and 160k miles is sitting right now since I don't have time to fix it, but I have to move it around and start it up to keep it from getting a dead battery and such, and it fires right up, even the day it was 18 degrees (which is like the coldest temp EVER where I live).
Does it crank slow? Does it crank at the right speed but take awhile to fire? Does it start then die? Can you keep it running with slight input on the gas pedal?
97 Mark VIII LSC/Silver/Gray leather
97 Cougar 4.6 Sport/White Opalescent Tricoat Metallic /Gray leather down but not out?
89 Cougar LS 3.8/Oxford White/Gray velour/HG need replaced AGAIN
00 Grand Marquis LS/Vibrant White/Gray velour
63 Falcon 302/black and rust/shed isn't moving
82 F-150/Oxford White/dumb VV carb doesn't pass emissions