My question is, other than foundation issues, which they don’t seem to have, what other issues should I be concerned about or look deeply into?

Limited is a max of 35k in repairs, nothing structural is allowed to be done (you can replace the roof put in a new kitchen, but you cant repair a foundation or cut a hole for a new window for example).   

If I hire an architect to help design & permits, get the foundation done by a licensed contractor, have Tuff Shed build the shell (they install it too), and if you can hire out subs to finish up the rest like electrical, plumbing, HVAC, flooring etc.. would self managing the project work?

For foundation I will hire a licensed co.

Unless it's near a university, no one wants to rent those.You will have much lower capex - there's no roof, no foundation, no gutters, no hot water heater, etc.

From a construction standpoint we have pretty much done everything other than pouring a foundation and hooking up utilities so it seems very doable to do this as the builder which would keep costs lower.  

There's also a property in that area similar build and original just like the subject property, for sale at $170,000 and has been listed for over 140 daysI am wondering if you comp the property just like you would with a SFR, this home was built in the 70's and has no foundation built in 1970.

Update:According to the inspector, the roof needs to be changed out soon because the shingles are cracked, some spots are showing the foundation that it is glued onto.

Approximately how much it can cost me to fix those foundation issues?

He can often be found at local networking events (not much help for you in the Valley), but you can also find him online.