While your ankle is mending ...
Fetch is a great skill for active dogs, especially if you can't do much moving yourself.
About the crating
Successful crate training takes hours of work and It sounds like your pup has formed a fairly negative association with his crate. If you want to pursue it I would suggest is trying to start fresh. Check Kijiji or Craigslist for a new used crate that you can trade for or pick up cheap. Dogs form powerful associations, but they rarely generalize - a new crate will be a whole new ballgame.
Once you have the crate, follow these steps
If you do not want to use a crate, but want to be able to put Thor in a puppy-proof room to be left alone for a while, this method will work just fine. The key is to break everything down in to small steps. That includes you leaving. Practice putting him where you want him to spend his day and go out of sight for 3 SECONDS. Come back and reward (as long as he has not reacted). Then 6 seconds. Then 9, etc. Work up to minutes. Work until you can stay in the next room for 10 minutes with no reaction. When you come back don't make a fuss, you also want to reward him for being calm when you come in. Ask for a sit, give him a great reward and let him out for a few minutes. You need to alter his emotional response to you leaving from "ohmygoshohmygoshohmygosh" to "well, I'm alone, but there are bones!" It's just going to take a little time.
In terms of things to leave him with, I am a fan of freezing food in kongs or other stuffed toys (you can mix it with a little wet food to make it smellier and wetter) and raw marrow bones (easily found in the meat isle of your grocery store). Make sure the good stuff only comes out when you are leaving him (including your training sessions while you are working on increasing the time and distance - i.e. "the good stuff comes out when I leave you, even if it's only for 5 minutes").
In addition to the bitter apple (rubbing it in his mouth is unnecessary - all that will do will be to associate you with things in the house tasting bad, and the goal here is for things in the house to taste bad irrespective of you) I would suggest picking up an enzymatic cleaner - this will de-nature the scent particles from the urine/feces and help to prevent your dog from marking over the spot he has already peed on.
Given his destructive habits and soiling issues my suggestion would be to confine him to an area that has a hard floor. Was he in the bathroom with the door closed? Gating him in there might make him more comfortable. What about the kitchen? Your pee-pad problem may be a differentiation issue (pee-pad vs. tile floor = easy, pee-pad vs. carpet, not so much). As you have already seen, punishing the behavior (or just showing that you're upset) will only make him avoid performing the behavior in front of you, it will do nothing to the behavior when you are not around. Dogs have no moral agenda, all they learn when they do something that makes you unhappy is that they shouldn't perform that behavior in front of you - not that what they did was somehow wrong. When he is caught soiling or chewing, just clap your hands lightly or say "oops" and redirect. This is close to what you were already doing, I'm just trying to suggest something as a-emotional as possible (I find it hard to sound upset when I say oops
It sounds like both of these (chewing inappropriate things and messing) are due to anxiety. My suspicion is that when you make him more comfortable with you leaving they will extinguish themselves.