Hey Spoo, I can help you with some of that but the rest will have to be GO replying to ya.
First, the chocolate sprinkles cake, pay close attention in NEI. There are two of them. One with a recipe, one without. The one with a recipe, of course, is the one you'll need.
Second, for the troll, if the knockback is the only part you're having trouble with, you can get a potion from the Apothecary in Draconis (which will come in handy later on during your playthrough with another boss). Using a strength potion also helps as you'll deal more damage per hit and get it over with faster. If he's doing some damage to ya, take a regen potion as well or some apples (the "notch" apple that's made with gold blocks and/or some jeweled apples). Probably wouldn't hurt to take a fire protection potion too cuz of the lava in the area, if your armor isn't already enchanted with it.
Now with the Nether portal, I never had that problem and I did create my own at my base, even tho I no longer use it thanks to Draconic Evolution's charms and I've never had that NPC teleport me there. The suffocating in the wall thing did almost happen to me with the Deep Dark though but if you break the area around you with a pick fast enough, you won't die. But the Nether portal that's near the Mystcraft portal, I believe, is part of a quest. I haven't gotten to that yet but I did find the exit portal in the Nether for it when I was flying around looking for cobalt and ardite. lol But as I said, I have my own portal too and I never crashed so not sure what happened to you there.
GO may be doing something about the antibuilders in the really dangerous areas as there's been a few complaints but I don't know. Will just have to wait and see what he has to say when he sees your post.
I do hope I helped you some though!