2nd gear loud clanking
 

So tonight I'm driving along, I shift into 2nd, accelerated, then I heard a loud rapid clanking. At first I thought it was an engine bearing, having just rebuilt the motor. Almost had a heart attack. But it didn't sound like an engine bearing, so I cautiously drove off, in first gear. When I shift into 2nd, I get a rhythmic clanking noise. Only 2nd gear does it. 2nd gear still works, despite the clanking.

If the car is coasting, and I step on the clutch, then gently press the shifter into 2nd without pressing hard enough for it to actually get in, the clanking starts and accelerates until it "matches" the road speed. The faster the car is, the more rapid the clanking.

Is it missing a tooth now? I was very close to home so I nursed it home and stayed out of 2nd. No other noises.

I hadn't driven the car for 2 months and only started driving it a few days ago. After this layoff the tranny was a bit difficult to shift into 1st or reverse at first; but after driving off it is OK. There is slight extra resistance getting into other gears the first minute or so, then it feels normal.

I had put in a new FM stage 1 clutch about 5000 miles ago, and the new clutch has always felt like you had to step all the way to the floor in order to shift, despite the adjustment procedure that FM specify which maximizes the pedal and slave cylinder stroke. If you were even 1/2 inch short of reaching the floor, it was hard to shift. (I also installed a new slave cylinder when I installed the FM clutch)

Could this have caused 2nd gear's demise? (I mean the recent difficulty getting into 1st or reverse when first driving off...).

Would it drive 25 miles to a friend's lift if I stay out of 2nd?

I have my doubts that the clutch is the culprit.

Drain the oil and see if you get chunks.

I broke a tooth in 2nd and drove it about 10km without any issues.

When my 2nd gear took a shit on me years ago, it did the same exact thing....except I couldn't use 2nd gear.

Mine did the same thing when I broke it at autox. I couldn't really drive it in any gear tho because the broken tooth would occasionally jam up in other gears and cause the whole tranny to lock up. I only drove it about 10 feet into the shop before swapping to the 6 speed

Definitely missing tooth/teeth.
My wrx trans did exactly the same thing when I shaved half its teeth off.

I have an extra trans btw, if you need one;)

Mine also died a similar death when the countershaft bearing went. Of course there was a lot of whining and squealing before hand, Then clunks, then death.