Transmission problems

I have a 1993 lincoln towncar that the engine ceased in and was replaced with a 1991 motor. The 1991 motor didnt match up to the 1993 transmission so I had to get a 1991 transmission as well, my father is an ex ford mechanic and he rebuilt my transmission 20+ times and still cant get it right. When its up in the air he and he manually shifts it he got it to shift 1st, 2nd, 3rd but when its on the ground it only stays in 1st gear when the cable shifter is connected (the 1993 cable is longer than the 1991 cable) and no my dad is on a long vacation should I say and left my car unfinished he told me to fix it and all I needed was a new linkage is this true? Will a new linkage fix my problem in order to get my car to shift properly or what do I need to get in order for it to shift properly please help me! This is my only means of transportation and I have 3 kids so I desperately need my car asap! Thanks guys for your help! Sincerely jessica