Looking for some help please - my chilli plants have several problems and I'm at a loss as to what to do....

1. I have a lot of seedlings sprouted in rockwool, and after putting them under LED lights in the last week or so they have gone green and it's spreading really fast across all my plants. 
2.  Some plugs purchased a few weeks ago have been in soil but have also now gone green and some are clearly growing some kind of mould/fungal thing (I see thin filaments in the soil which I'm certain are not roots). Also some of these filaments have been seen on the rockwool.
3. Some plugs went purple after potting on (they arrived as coir plugs, all leaves green) and I suspect there is a phosphorus deficiency due to root shock. I think this has started to improve on new shoots when I fed with a 50% strength of my 18-9-9 tomato/chilli feed. The only thing I'm slightly unsure of is that mine are really purple - most of what I read about phosphorous deficiency says leaves "start" to turn purple on older leaves but mine are 100% purple to to bottom.
4. Some plugs have darker parts on the middle of newer leaves - no idea what this is?

  
Possibly relevant info. It could be reusing materials from last year has caused problems and introduced pathogens:

* I used water from a butt which possibly has stuff growing in it (it wasn't cleaned from last year).
* I used plant food left over from last year, although it has been stored in a dark(ish) cool(ish) place.
* I used perlite in the soil mix which was stored from last year which was in a woven plastic bag, and which has been wet so possible this has grown mould/nasties.
* I used left over seed soil from last year which was in an open bag.
* This is my first year using rockwool. I've used coir pellets before which worked fine, but I thought I would try rockwool as last year I purchased a mature chilli which was started in rockwool cubes so I thought I would try it. Perhaps this is a mistake and I've done something wrong?
* Last year I used 2x55W T5 lights for this stage, this year I upgraded to 300W LED lights (currently 50% @ about 12 inches). Intent is to move to greenhouse in a couple of months or when the plants get too big for inside.

  
If it looks like I've infected my plants with nasties should I just dump all the left overs from last year and re-pot the plants? I think for when do plant up the rockwool I will not reuse any of the stuff above but start again with a new mix.

Help! Having serious problems with my chilli plants and worried I may lose them all.