If you've already got the trans in and clutch slave cylinder mounted yadda yadda yadda, I'm guessing those are the bolts that hold the shifter assembly down (inside the car) and possibly the clutch pedal as well.

I'm almost positive thats how it went, I bought my MTX off Terry here and he included a baggy with pretty much the same exact set of bolts and I used almost all of them inside the car.

Just start on the outside and work your way in, its not too difficult to figure out once you get the pieces in place, just use process of elimination.