transmission

If it was the linkage wouldn't there be a problem all of the time? My problem is after I shift it into drive and it shifts from 1st to 2nd it feels like it doesn't want to go into gear, but if I drive it after its been sitting all night it doesn't act up untill it warms up

check the fluid level...warmed up and in Park with the handbrake set~ sounds like perhaps the fluid level is slightly low~

Fluid is topped off

no....topped off is the WRONG answer...warm the engine....put it into park....set the parking brake....turn the engine off....pull out the transmission stick and look at the level when you put it back in....smell it to make sure that it hasn't overheated...make sure it's cherry red...perhaps you've started a leak with over-filling that~ remove a bit to make the level TO THE LINE~ mkay~?

By topped off I ment that after I changed the atf i filled it to the line that said ok on the dip stick then drove a couple miles and then checked it again

okay, we've established that it does not bleed automatic transmission oil...but in my experience, if trouble engaging a gear or two is the concern...it is always the links that operate the selector...as I've stated you've worn bushings...hearing a crunchin' sound, you may need a new transmission...just one man's diagnosis~ like I know several things about automatics...when they leak coolant is going to be from the radiator connection...Black fluid means that unit was put through the paces..."cooked goose" is what one might say, shift points and shifting can be affected by adjustment points...but not if there is no way to adjust or affect the performance...I believe yours is straight forward...follow your shifter's control to the transmission....this is where the trouble lies~ high mileage would show MORE wear on the links~