Ok here is my scenario...

This is my first winter w/the swap.

1999 EX Automatic.... I swapped the trans to manual EX over the summer.

Everytime the weather goes below 30 Degrees it takes at least 40min before i can put my car into gear. I was driving home today on the highway after 1 hour and my car would not go into gear. Any ideas?
On a normal day 40deg+ weather it drives fine... Happens when it gets cold :-(

Is the clutch dragging?

Try bleeding your clutch slave cylinder. As Chiovnidca, it sounds like the clutch is not fully disengaging. Can you engage the gears with the engine not running?

Even with the engine off..i have to jam it into gear...and sometimes that doesnt work until 45min later.....

If the car is in 1st gear and you start the engine, does it creep forward on a flat surface with the clutch depressed? Does you clutch pedal feel different when the gears will not engage?

What fluid did you use in you transmission?

Clutch feels the same when its in gear and when it is not..

Does not creep forward when it is in first.....