I had a couple for al..
1) I kinda found the answer already in pg 88 so im half way there but heres the situation. I started seed which were in a propagator/cover until roots sprouted thru the rockwool. Then transplanted the small plants with thier rockwool plugs into 5" square pots filled with hydroton pebbels. But before I was thru, i soaked the rockwool with the newly mixed solution it will be receiving. On top of that I was filling the table almost all the way to the top, saturating the rockwool again 6x/24hrs.. What i have now is some of the plants with yellowed bottom leaves, with blotches and overall stunted growth compared to others. Will these plant eventually recover and strive just like the rest by just letting them dry out, or are these scarred and will show the signs of f***up in the future?
Good onya, you've found the fault.
Yes, if you have corrected the flood level problem, they will recover, but will be slowed a bit until they catch back on. Hopefully, these are still vegging. If they are in flower, they may not have enough weeks left in the flowering cycle catch back up to the others. It's cool, you'll know better for next time.
I also have a flood cycle at 2am when the lights go off at 12am. Is that totally wrong?
2 hours
past lights off? No, you don't need to water during lights-off at all.
Best not to water immediately before lights-off, too. If lights-off is at midnight, your last watering should be no later than 10-10:30pm.
Also I have heard that you should keep on lowering the flood level as roots extend down into the pebbles. Is this so? And if so, at what point do you stop lowering the level?
No, it's OK to flood roots in pellets because pellets don't hold anywhere near the amt of water as does rockwool. There's lots of airspaces between pellets, so you can flood really quite often, about 3x per lights-on in wks 1-2, perhaps 4x in wks 4-6, perhaps as much as 5x in the later weeks.
Last one... I see you use a HPS for vegging. Any particular reason? Do you use it to get your length on clones faster? I just ordered a Sunmaster Cooldeluxe for $89 compared to a standard MH for $49(and more lumens for cheaper). Did I make a mistake with the lights also?
I initially used the 400HPS for vegging mums because it was on hand. It worked a treat so I never bothered getting an MH.
Several years later, I did pick up a MH conversion lamp for HPS on a whim (got it cheep). Used it for about a month- and it did exactly what an MH is supposed to do, surprisingly enough.

Veg growth was much mode compact, internodal lengths much shorter. You'd think that was good news, wouldn't you?
However- it meant that I didn't have nice long stems for my SoG style cuttings... so I switched back to the 400HPS... and the MH conversion lamp sits on the shelf.