Wow! It sounds like you had a really tough time with this map! I won't argue that it's a tough one and there are places where you could use a shield regenerator or power-up, but the only major problem I had with it was when it contained lava f'lickta. These beasts are immune to lava and this is an extermination level - you have to kill everything to leave. That exit teleporter will not activate until you do. Since a lot of the f'lickta were in the lava and the only way to kill them was with your fists - well, I think you can see the problem. My very strong advice to Forrest is to remove the extermination flag. This level is difficult enough and the point is only to create a diversion - not to sterilize the facility. Besides which, it's a bit weird to have a transporter not work just because you haven't killed everything - at least with a terminal, you can tell the player that they have more work to do.
For the benefit of everyone else here, you don't need to do any flying to finish this level at all, but you do have to do a fair bit of swimming through lava. Getting through that repair switch is one of the trickier moves in the scenario. It's been a while since I played this level and I'm going to go back and try replaying it tonight if I can, so I'll be posting more later, but as I recall, there are some nice secrets here, and there are some intriguing places that I could never seen to get to as well.
Oh, and Viscera is a term that refers to your hollow organs - basically your stomach and intestines or, in lay terms, your gut. That's where we get the word "visceral".