Hi and welcome to BinkyBunny!
Bunnies by nature don’t tend to like being held at all, and unfortunately there is no magic formula. Try to think of it this way: Trimming nails is a necessity of daily care and health and it needs to be done no matter what. Try to make to make him as comfortable as possible because really, a bunny just needs to get used to it. I know it sounds cruel but thwen you are ensuring that they are well cared for and their health is sound, sometimes you just have to brave it, otherwise you’ll need to take him to the vet to have it done. Hurt feelings are nothing from your the bunny compared to what could happen (offer a treat afterwards) and they will forgive you.
What I have done in the past with my two is dose them with Rescue Rememdy (Bach flower essence), give them a mini-massage, burrito them and trim (be sure to have long sleeves or a smock on with them and a heavy towel or blanket in your lap. It sounds like your guy is not going to sit still for the massage so you may just want to head for the bunny burrito method. Keep a firm hold on him too and if you have to trim one or two nails at a time, then do that. I’m sure he’ll sulk afterwards and give you an ostentatious thump, but know you did it to better his life.
Your guy has had a past with lots of change and different enviornments, who knows what he has been through maybe kids picking him up and accidentally dropping him (it’s really hard to say) or someone who pulled his ears. It takes a while to earn his trust and try bonding with him if you’re up to it by just sitting or laying on the floor by him and if he comes up to you, offer up a treat so he knows that humans aren’t bad after all. He’ll soon warm up to you once he knows that you’re OK and this time the home he is in is permanent.
Also equally important here, has he been fixed at all? That could also be why he is so squirmy as well. If a bunny is not fixed they can be quite a handful and I highly recommend finding a bunny-savvy vet and having him fixed (and nails trimmed too if you are not able).