If you have plants in 3.5" pots that are putting out fruit, then you really are late in potting up. But all is not lost by any means. They should be fine now that you finally got them repotted. They were likely severely root bound so what you should have done if you did not was to break apart the root ball and let the root system loose. If you just pulled the plant out of the small pot and dropped it into the bigger pot, the root ball will take some time to figure out that it has a lot more room and will stay root bound for some time. The Big Jim just took to the new pot better, but the Black Hungarian should catch up. If you are concerned, you could always pull the BH and spread the root ball out a bit and replant it.
Bruce

You will see this inability to recognize that it is in a larger pot if you started in a peat pot and transplanted leaving the pot on the root ball (as the manufacturer suggests). You would need to take off the peat pot.

Otherwise as per Bruce above.

Dennis

Hi Bruce and Dennis,

I really appreciate you taking the time to answer. Thank you for your help and insight!

Mike

Yeah, if they're root bound (as in, you take them out of the small container and you can clearly see the roots wrapping around and around), you need to break that ball up.

Just kind of dig into it with your fingers and pull it apart kind of like an orange.

While you obviously want to not rip all of the roots off, its actually very difficult to kill a pepper from physical damage, so don't worry about being overly cautious. Long as you keep most of the roots on there, it'll be fine. Might look a little sad for a day or two, but it'll perk right back up pretty quickly.