Hello and welcome. Glad to see you.

I've always wondered how that system would do for growing weed. I hope you will continue to post your thoughts and results. And we all like pictures.

1. In the past week I have noticed some light brown spots on the leaves. (see pics) Anyone have any idea what these are? Also, can anyone recommend a commercially sold nute solution for the rest of veg and also flowering?
That is a problem that I've not personally had, nor am I'm not familiar with it. I have posted several problem charts that could probably answer that question though. Advanced search with my name and "problem charts", and choose to search titles only. You should get at least 3 this way. I highly recommend saving these to your computer in case, God forbid, this site goes away like overgrow did.
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For the nutrients I firmly believe in SuperThrive and Fox Farm stuff. For vegging I use Fox Farms Grow Big, and Tiger Bloom for bud. For additives, it's ST and Liquid Karma for veg, and Fox Farms Open Sesame, Beastie Blooms and Cha Ching for budding. However, you don't need all this to make nice big nugs. For a while I used no additives, and got great results. I recommend not using many for your 1st grow.

2. The hanging part of the roots are submersed in the reservoir, is that bad?
Your roots need both oxygen and water/nutes to survive. It is great that at least some of your roots are in water. That way they wont die during a power outage. However it is also great that some are in air. It is best if they could all be in air, getting wet from popping bubbles, but it aint going to happen in your set-up. Once you switch to HID lighting that res will get completely filled with a tangled root mass. This is not a problem, just a fact.

3. Should I be emptying the res every few weeks or so, or should I just add water/nute as needed?
Yes, by all means you need to do a res flush. Depends a bunch on the system, but at least once per month. I would probably do at least twice per month on yours.

You absolutely made the right choice about the lighting. 400 is a lot for that little system, but that's probably what I would want. Just be sure to keep the light pretty far back (2 or 3 feet at first, while your plants adjust, then eventually you'll want it as close as possible, but change in stages maybe once per week. Also 400W HID makes a bunch of heat. Have you thought at all about what you are going to do with it? You almost need to vent this to the outside somehow, but you may be able to figure out how to cool without doing so.

Good luck, and please keep us posted.

OP