What is wrong with my transmission?

Hey guys. I just replaced the 700r4 transmission in my 88 GMC 4x4 with a used one that has about 80,000 miles on it. When I first fired it up last night, it made a horrid grinding noise in every gear but park, and my truck would not go anywhere. Today, I put more fluid in it (up to about 7 quarts total), and put the transfer case in neutral, and re-adjusted the transmission shift linkage, and after doing that I got it to stop grinding in every gear except park, which still grinds. None of the gears will catch and it still just sits there. A couple things to note though is that I have only 2 bolts fastening the flex plate to the torque converter where there should be three, and when I dropped and replaced the transfer case it was in 4H. Could it be that missing bolt? I have heard several answers on that. I just don't know, any ideas would be great. Thanks