Newbie - Capsicum with yellow stems

Could really use some help and advice for a Chile Pequin I have.
 
I live in Austin by Lake Travis. I moved away for 6 months, leaving my potted plants at the house. I finally got my plants the other weekend, and they were in awful shape. Some were dead, some just in bad shape. Looked like they were neglected for 5 out of those 6 months. All I have left is a Pequin plant that is half thriving. 
 
The back yard where I had my pots, was kind of a mini valley. Had a limestone hill 20 to 30 feet high, as high as the two story house. At the bottom we had our car ports and grass yard. I had my plants scattered all around the yard. The morning sun would hit the yard from sun rise to 2pm, then the shade would take over.
 
All the plants were left uncovered, outside, and weren't trimmed back for winter. So winter passed and its now April. It just looks like one side of the plant got sun, and it was never rotated. Half the plant is lush, leafy, and green. The other half of the plant, well the stems look yellow/green, and the leaves look stunted and not new in growth. It looks bare and naked on the side with yellow stems. It even made two peppers on the yellow side, but they didn't mature in size. Poor plant thought it was dying I'm guessing..
 
I am giving it as much sun as possible, and when I got the plants or plant, I gave it some fish emulsion. Should I trim any of the yellow stems off? It would literally be half the plant, and just wouldn't look right in my eye. But that's why I'm asking for some input. I don't know if it's lack of sun or over watering from rain. But I almost lost a total of ten plants, so I really want to help out this Pequin.
 
My serranos, purple tepins, yellow tepins, and even my native texas tepins dried up and snapped like twigs. Unbelievable.
 
I decided to keep 2 of the Tepins, the worst that could happen is they never grow back. I won't get my birthday taken away.

Hey Tex it's hard to say without seeing the plant but if the yellow parts are looking kind of necrotic it would be a good idea to trim off the dead parts. Any chance you can take a picture and upload it?
 
Also hate to hear about the loss of all your tepins. I wouldn't give up on em just yet though. When I've left native tepins out over winter they usually die back and look dead then regrow from the stump in the spring time. I usually just wait til they look dead then trim em down to a couple inches tall.
 
We didn't really have any hard freezes here in Austin this year so they might pull through. I think we only had 5 total days where the temps dropped below 32. 

Welcome Textep! Hope your plant pulls thru for you. I don't think a trim up will hurt you any on the pequin especially with new attention give to it. Don't give up on the tepins! I've had some sport new growth down near the soil way late. I always leave mine out too.

Good luck

Mike

Hey guys just a little update and info on what I've done.
My pequin is doing well. Never got any new growth or signs of improvement on the yellow stems. I trimmed back the stems and left a 2 inch stem. It is now filling in it's bare side, but the growth is slow, and it's coming from the bottom of the healthy side. On my next watering day, I'm probably going to give it a good soaking.
 
I had two wild Chiltepin's. One in potting soil and one in a texas limestone soil. They weren't showing any positive signs, so I up rooted them, carefully, and put let them in a little tub of water. I added fish emulsion, a banana peel, and vitamin b. Within 24 hours, leaves came out.  One plant is doing well and is now in a pot.