CT requires an Architect (or Engineer) for projects of this nature, especially a building of this age where it's likely there's structural/framing items to address.

I haven't met her yet, but can only expect a request to come out of this as well.At the end of the day, I want to address the basic needs of my tenants, but I can't help thinking that either that people got word of the original showerhead I replaced, or they're just taking advantage of the rent increase.

Just pick up the phone and call the subcontractor and give them the address

Hello, I own a duplex with two separate addresses.

Since I'm a BP member and have used the "getregistered" site before to register for last year's conference, it recognizes me as having an existing log-in, but will not let me move past entering an email address to actually register.

This implies that the city cannot demand the removal of an unpermitted issue and any red tag on an unpermitted unit unrelated to safety you have 5 years to address.  

We just had our inspection done, and there are some things that need to be addressed, for one, there is ongoing water intrusion due to no roof flashing, or chimney flashing still existing.

@Alex Sarnoff, Much of your uncertainty on these things can be easily addressed by your QI. 

For example, I thought rent-controlled tenants would have significantly longer stays, but they were 10% to 20% more likely to be at their 1994 address 10 years later.https://journalistsresource.org/economics/rent-control-regul...

Consider all the things that could go wrong and see if the lease addresses them: unauthorized pets or tenants, early termination, security deposit, lease violations, late rent, eviction, lawn maintenance, parking, etc.5.