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Post transplanting questions

I transplanted 2 weeks ago from solo cups into 5 gal root pouches with a mix of ProMix, compost, and additional perlite, plus Osmocote per instructions and a few tablespoons of bonemeal at the root base.
 
My plants overall look really good, but I have a couple questions complete with pics!
 
Long internode on new growth since transplant:
 
When my seedlings were in the solo cups I went a little heavy on the ferts and had some leaf drop, stunting, etc. I think I got nutrient lockout and/or salt buildup despite flushing the cups (not sure if this is necessary info but just providing background).
 
Since transplanting a couple of my plants have a ton of new growth, but there are some pretty long internodes and I'm wondering if I should top/prune them or let them ride. Also, notice the stem is darker in color and the stem is stiffer/woodier - this is the indoor/stunted growth. The new growth is green and limber on top. See below:
 
Red scotch bonnet, new growth on top is long.
 

 
Same thing on the cayenne (first) and poblano (second) and jalepeño (not pictured)
 

 

 
1. Is this bad? Should I top them to thicken the bases? I'm in Northern California and should have lovely weather through September and into October, keeping the pod maturation time frames in mind.
 
My jalepeño has light lower leaves but healthy looking new growth. It is my only plant like this. I've looked at the images for nutrient deficiencies and can't quite put it together.
 

 
2. Is there anything I can or should do about this?
 
My plants are in containers and the side that gets more sun seems to be growing a little faster than the opposite side.
 
3. Should I be rotating plants on a daily/weekly/x days schedule? 
 
Last question, thanks for bearing with me!
 
4. This may be a stupid question: when you top a plant, does the main stem/trunk stop getting taller at that point and only thicken? Or will it continue to get taller but at a slower rate as the other branches thicken and grow faster?
 
If you want to copy and paste this little section for you answers, here you go!
 
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Thanks!
 
If new growth is green then USUALLY the yellowing older leaves are normal.
 
There is probably a longer internode on your main trunk since transplanting from more root growth instead of main stem growth. I got some clones and they did the same thing. 
 
The older part will turn woody. This is normal.
 
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