I swapped in a 01+ 6 speed in my NA last month.
When the engine is warm (I assume the transmission is warm as well) I can get into gear very easily.

However, since the weather has cooled off it's really hard to get into gear (especially reverse) after a cold start.

If I do manage to get it in gear after waiting for it to warm up, it starts acting normal, but i can not get the car to move after cold start and have to wait till it will let me select 1st 2nd or reverse. Usually it's less of wait to get it in the forward gears so these days I started back parking the car.

I believe my hydraulics are fine because when the car is warm I can get into any gear easily. Fluid flushed this spring and new slave cylinder put it as well at that time. (I put in redline mt90 when I swapped the transmission in last month)

I have FM level2 clutch kit for what its worth. (it engages/disengages very close to floor)

 

Have you tried adjusting the clutch pedal linkage to make it engage more towards the middle of travel?

 

The level 2 FM clutch can be a real bitch to get enough pedal travel. The MT90 isn't helping anything either. Get the motorcraft or Amsoil juice.

 

what these guys said: adjust the clutch and switch to a more temp friendly fluid.

for what its worth, my synchros are real finicky when cold as well. it goes into gear, but can grind if you don't do it just right when dead cold.

as soon as warmed up, its buttery smooth

 

+1 ^. Every miata 6 speed will clunk a bit until it warms up. Cold ambient temps just make it worse. Adjust the pedal, change the fluid and hope for the best.