I just got doing this. Blake, you are right. There are bolts that are holding on the bell housing that are under the flywheel. You will need to take off the pressure plate, clutch plate, and the flywheel to get to them.
To get to the pressure plate bolts that are up on the top behind the bell housing you will need to use sockets, then knuckles (socket extension knuckles), before your extension and wrench. You may need to pull the transmission (I think you said you have done this) and the shifting fork to get to the bolts but it can be done. You will need to go through this shifting fork hole to get to one bolt.
Then you can get the flywheel bolts off. When the flywheel is off you will see the top bolts.
You shouldn't have much of a problem. Just take it easy or you will loose skin off your knuckles.
Have fun.
