92lxtrunk

I bought a 4 cylinder conversion car this past Saturday. It's a 1992 Mustang LX 5.0 5-speed trunk car. It has a motor/transmission out of a wrecked 1989 Mustang. Has mass air and everything. When we went on a test drive the very first time I shifted into second it grinded pretty bad but never did it again and all other gears worked perfectly fine. It did it just that one time. That led me to believe that it had the wrong fluid in it. I drained the fluid from the transmission and put Dexron Mercon III back in it like it calls for. Now the car is hard to get in any gear. Sometimes 3rd won't go in at all it'll just grind and pop out unless I try to force it in which I don't like doing. I feel like I shouldn't have messed with the fluid The fluid that came out of the transmission was red so I know it didn't have gear oil or anything in it. Some people are saying it could be my cable or the pressure plate. It has the stock clutch cable in it. What could be the problem? It's such a nice car other than this problem.