I just swapped in a 2.3 out of another '90 mustang (guy was doing a turbo swap). It runs great, I did new water pump timing belt plugs etc. When I get in and start driving everything is just fine and dandy, but after a while it doesn't want to shift into gears while the engine is running. Turn it off and it'll shift normally, but if its running reverse wants to grind like there's no tomorrow, and 1-5 just dont go. If i'm moving its ok too What can I look at?
I am assuming its a manual but check your clutch cable, failing that you will need to look at transmission oil, then clutch/flywheel. Easiest way to check fly wheel is to drop of the starter motor and carefully get one one to manual turn the engine. Just don't mess up your timing.