i put in a used transmission in my 1990 lincoln town car signature and now when i try to put it in gear the shifter isnt right

Are you saying that the "D" does not line up where it did before. That's just a cosmetic thing and can be fixed at a fairly low cost, but, honestly if that's the only problem, I would skip it. It's a 1990 car. Now, if it's something else, causing a system malfunction, I would get rid of this car. The car is 26 years old. So, what's going on?

If I'm correct, as Mark said, the shift indicator is cosmetic. It's basically just so YOU know what gear your in. This could be important, because you don't want to be running around in say, 2nd gear; you'll blow your trans. Anyway, the indicator should just be as simple as adjusting the linkage from the shifter, to the transmission. However, I'm not 100% sure, because I'm not quite sure how the shift system is set up.

Smashkin666- yes, well, it's a 1990 Lincoln Town Car, and most likely they will just pull the shifter into gear from park and leave it in drive for the duration. I had an old 1985 Thunderbird, and the shift indicator was off by a little, didn't affect anything at all. This is not the kind of car that you're going to downshift often. Besides, on most Fords, if the car's in second, you'll know it right away. Every Ford I had in gear 2, actually started in 2nd gear rather than 1st. It's a Ford thing to give you better traction. With a little trial and error, your going to know where the right place is for normal "drive".

Oh, yes. I completely understand. That's how my pickup truck was, until, of course, the column blew out.