Extreme knock to my confidence? How to get back into the saddle without second guessing?

I think it's a terrible idea to put him in a pelham just because he has started rooting at the bit. That will definitely only intimidate him and could easily cause more problems. Almost any horse at the early part of their training will pull on the bridle, only because they haven't learned not to yet. Are you riding him in a snaffle now? If so, that is what I would keep him in. Try riding with more contact. Not necessarily a tight rein, but enough that you can "feel" his mouth, but still release him when needed. When he roots at the bit, don't let him just take it from you. Hold your hands as steady as possible and ride him up to the bridle with your legs and seat. If he gives to the bit, release him. Do this constant take and release and he will eventually learn not to root at the bit, but to actually collect up. Do you have any videos of you riding him? Or do you have the availability to get one? I would be glad to critique you, and help you any way I can. I've started literally hundreds of young, unbroke horses and got them to the point where they were winning in the show pen. Hope this helps, good luck!