You probably need to water less...oxygen to roots is just as important as water to roots.

They could probably also use a dose of fertilizer (or a half dose) that's high in N.

Lower leaves that are shaded out by top growth commonly yellow/die and fall off. That's normal. It's also caused by N stress taking N from older leaves trying to use it for new growth.

I fully agree withs nc - crn

I agree about too much water, but am not sure they need high nitrogen fertilizer. Too much Nitrogen now will just put on rampant top growth and it's really too late for another fruit set anyway. I'd recommend some well balanced fish emulsion on a light dosage (I prefer organic fertilizer). And let the soil dry out just a little between each watering.

Go ahead and pick the peppers that are fully orange, that's what you are going for. All peppers ripen from green to red/yellow/orange sooner or later. Thats when they are the sweetest and the best to eat. Once you pick some peppers the plants will likely grow a bit more.

As far as the ones that are rotting, you can cut them off and eat any salvageable pepper from them. It's common to lose some peppers from blossom end rot.

Good luck,
-Mark

About picking, agree with Mark. The yellow ones are not going to get any bigger. So there no point keeping thenm on the bush., Unless you except and want then to turn red !