So I bought a 1990 f150 that was told was running when bought. During the tune up we found blown head gaskets. When I set the mark for tdc my cylinder 1 intake valve is still open. What am I doing wrong or not doing right.

 

180 deg off maybe.
Cyl #1 is passenger side front.
Remove the spark plug and and rotate the motor with a breaker bar until the piston comes up to TDC on the compression stroke, air will be pushed out the plug hole when this happens.
Use a piece of rigid wire or a small straw placed down the plug hole to feel for exact TDC.
Now check the crank pointer, is it lined up on the 0 mark?
If so you're good, if not the timing set isn't installed correctly or the balancer outer ring has slipped.

 

Crank rotates twice for each cylinder in the firing order. You're 180* off.