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health First time growing from seed, couple issues (burnt edges, brown spots, etc)

**Kinda long, but I'm a first time grower from seed and would appreciate the help! I did search first, and got a few answers, but would love some additional help personal to my situation :)

Ok guys so this is my second year gardening, first year from seed. I've got 10 different varieties of chinese and 12 varieties of annuum (and a baccatum thrown in for good measure, aji amarillo).

Hots started to germinate and got potted up to red solo cups around the middle of Feb, on average they are 8 weeks old at this point.

Annuums and baccatum were about 4 weeks after the hots, so are only about a month - 6 weeks old at this point.

Gardener's Supply germinating and transplanting mix. Gardener's Supply PHC (plant health care) fertilizer used maybe 3 times so far, and not until plants had at least a few sets of true leaves. Waterings about weekly, I wait until the soil at least dries out on top, sometimes I get busy and don't get to them until a day or two after I noticed the soil was dry (by that time they've got a little wilting going on, but nothing major and they always bounce right back up by the time the watering is done). Bottom water every time.

Here's my three main problems so far (everything was going great until about the last 3 weeks):

1. A decent amount of what I think is fertilizer burn on a majority of the hots. Browning edges, brown spots on the leaves, etc... The hots were the first ones to get a dose of the PHC since I started them first, and the first watering with the fert I think I overdid it a bit. Noticed a few days later I had some browning going on. The majority of the browning is on the hots alone, which is why I think they got overdosed the first time around.

2. Some light colored AND dark colored spots on the annuum leaves. The brown spots I think are fert burn as well, but it doesn't quite look the same as the brown spots on the hots. The light colored spots I have no idea about; they have the same pattern as the brown spots, but instead are just really light, light dots on the leaves.

3. New growth is coming in really light green, and some of the leaves on the annuums are pretty pale overall. A couple of the hots have light green edges as well. I think this is all overwatering; the holes I punched into the bottom of the cups weren't the biggest, which is why I'm potting up to 4" nursery pots out of the solo and styrofoam cups.

On that note, the first round of potting up to the 4" pots came with the hots this weekend. I had to do some pruning of the roots as they were getting somewhat root bound in the solo cups and without some pruning I couldn't manage to get them to "sit" correctly in the 4" pots. After I got them all potted up I did a bottom watering with a VERY light application of fert. Thing is, over the next couple days I've noticed some additional fert burn, and some of the previous spots got a little worse. I'm thinking the shock of transplanting along with the pruning of the roots is what caused the fert burn with even a really low dose.

So I think I have some fert burn, I think the cups aren't draining well enough, and I have no idea about the pale green dots as opposed to the brown ones. I'd just like some additional thoughts on this and I'm hoping they'll all pull through!

LINK TO A BUNCH OF PICS http://photobucket.com/pepperproblems
 
I find new growth is usually light green then darkens slowly. Also I had a couple of my lower leaves brown and fall off as well. Its not a major issue and may be in part to transplant shock. As long as you are getting new growth you should let nature take its course and not worry too much.
 
I really take encouragement from NSizzle's suggestion. Since I transplanted, my plants have really been going downhill.

Lots of wilting, lots of yellowing. I'm pretty sure I overwatered, probably too much light, and I imagine the MG soil I transplanted them into is releasing too much fert for such young plants.

I'm opstimist though.. since they are still alive and continue to produce new growth, I'm hoping that the natural resilience of peppers and nature will work it out in due course.

To quote the Black Knight of Ni.. "It's merely a flesh wound! I'm not dead yet!"
 
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