Hey chad, no need for apologizing for the length of post, personally i think the longer more informative the post, the easier it is for us to accurately help you diagnose the problem.  I'm not a hydro guy, but my experience with auto's is is that they sometimes act weird, like grow slower sometimes (mostly cuz they are growing like crazy underground), I had one one time that the cotyledon leaves stayed for like 3 weeks and got huge with no center growth in sight, that plant ended up yielding like 6 oz's.  And I don't think you did anything with the Fox Farms at full strength either, cuz your plants would be burnt up (I would think).  And Fox Farms charts their ppm's are way more than any other nutes that i've used, and i have heard a lot of people talk about how hot FF is, I personally have never had a problem and have always started full strength from seed and growing in FF Ocean Forest and in coco coir.  Oh one more thing, I always double check my ph pen against some drops just to make sure it's calibrated.  Only saying cuz the brown spot thing sounds like cal/mag which would be due to it not being available (ph), seeing how you said your adding it already.  Good luck man, happy growing.

Yep keep an eye on the ph pen! I just had problems and it ended up my ph pen was off which caused me to have to flush for 3 days and redo a 30 gal reservoir...real pain in the ass for just a small thing that could have been caught if I had stayed on top the the calibration!!!