However, it seems like as long as you keep the two separate, and always disclose you're an agent there shouldn't be a problem.   

The buyers agent works for you as a fiduciary.A dual disclosed agent essentially tells you that they now represent the interests of neither the seller nor the buyer.

You need to disclose that you are licensed.

ADUs are still fairly new on the east coast so there's no precedent for this kind of thing that I can find i.e. using a Homestyle loan as an investor to build a new, detached ADU.The downside of the investor choice is I can't legally live on the property unless I disclose this to my lender.

The home had severe structural/foundation issues which were not disclosed in that pre-listing inspection report that was sitting on the kitchen counter during our buyer's inspection.

I have a totally separate LLC to invest under, it won't be in my name... but I will still be obligated to disclose my license status, right? 

B/c it is such a great deal for my area, my agent is going to try to get the asking price down from 287k to around 260 or to see if they will pay for the fix ups since they didnt disclose any of the dangerous hazards on the seller disclosure, If the seller isnt willIng, then Im out.

In Texas the purchase amount does not have to be disclosed, apparently.

Further to the point above by @Jeff Cagle, California's almost-mandatory disclosure, the Real Estate Transfer Disclosure Statement, asks the seller in C.12. to disclose whether there are "neighborhood noise problems or other nuisances." 

Well that same neighboring house is now under contract and I'm concerned that the selling agent may not have disclosed that the driveway isn't communal.