2004 4x4 with 4.0 and 5 speed manual. intermittent hard up shifts, especially 1st to second gear. Never does it when cold but after things warm up it will sometimes be hard to get into second gear. Always on up shift never a problem down shifting. It does not grind, just will not go into gear unless you really pull hard or jerk it. What is going on??

 

I would plan on changing the fluid just to see if that helps

You have an M5OD-R1(M5R1) model transmission, it uses ATF, yes automatic transmission fluid in a manual trans
Spec was Mercon V
Some people say synthetic makes shifting easier, certainly won't hurt to try it
It holds 2.8 quarts bone dry, so may only take 2 quarts on a refill
And yes you can mix regular and synthetic, no issues with that at all

Drain and fill holes are both on drivers side

M5OD-R1 was used in Rangers from 1988 thru 2011, they are engine and drive specific
An M5R1 from a 3.0l will not fit on a 4.0l
A 2WD M5R1 can't be used in a 4x4, or visa versa