So I was driving the car today and I found out it only has trouble shifting when the car has been running for a while, but when the car cools down or its cold it'll shift just fine.

 

No sir. You are putting 155X the strain and wear on the syncros by holding the shifter to a point where the car creeps forward.

 

Have you checked or changed the tranny fluid? From Billman's description of what you are trying... maybe the tranny oil got burnt.

Just a thought...

 

My tranny fluid is full and my clutch fluid is full. Ever since I flushed my clutch it's been acting up more and more lately

 

I'm gonna put $5 down that the issue with your slave.

 

Hmmm really sounds like you got air in the lines then. When you bled it, did you remove the slave from the car, and point the bleeder straight up in the air? Did you gravity bleed it?

 

I jacked the car up and pumped the clutch

 

Try it Billman's way as I described, let us know if that helps. 1/4" clear fuel hose is your friend. For the record I've never gotten all the air out of the line by pumping the clutch. Gravity bleed is the way to go.