Throughout my studies I kept hearing this nightmare stories from professors and professional architects about the headache that is working with clients.

Not exactly the same but similar.To do something like that you're going to probably need to work with an architect and definitely get the approvals from your local county.  

Architect?

Would I need architect plans since it is all framed already?

Hello BP gurus,I have a duplex that's over 3500 square feet, with a large partially finished attic that appears could easily become a third unit, though it will need a fire escape for a second egress.I would need zoning relief (variance) from the local planning board to become a triplex (there are a few larger multis in the neighborhood), help from an architect on design and code compliance, and a general contractor to build it.

I’m a registered architect.

Add to the mix the utilities, architects and engineers and it is easy to get bogged down.  

I was told to get an architect and structural engineer and they will let you know what to fix as the process will require permits and inspections so walls will have to be open.

If you do need stamped plans, then find an architect asap!  

Although the architect should have caught this IMHO....