It's tough to micromanage, but peppers are damn resilient. I ran in to the same problem last year - kept 40 plants alive all summer in 6" (3/4 quart) pots. Most ended up becoming my overwinters - I still had two alive, as of last week, in those original 6" pots. I *finally* gave them a new home yesterday in 15" pots - lost 5 of my bigger overwinters and recycled the pots for smaller ones
So that's 11 months they lived in 6" pots, root bound .. root decay... bad soil.. no nutes.. .transplanted them and hoping for the best. Been propping them up on nutes but they were showing very bad iron, magnesium, and calcium deficiency. Nasty gnarly leaves with all sorts of problems.
Hoping they pop back now that they've got fresh soil.
Try as I might, the ONLY way I've killed pepper plants is overwatering and leaving outside to freeze to death. Nothing else seems to work.