Transmission issues shifter not working properly?

When I put my truck in drive it is in neutral so I put it in 1st and it goes to third but I have to shift it as I drive but it won't shift into over drive I just changed this transmission out with another used one and I am at a loss of how to line everything back up the way it should be so it will shift the right way. If you have any advice on what I could check or try to do I would greatly appreciate some help.