That is much cheaper than the minimum of $2,000 I have to pay just to swap out an existing gas furnace, assuming there are no alterations required for the duct-work and vent systems.$1,000 buys a LOT of insulation. 

They were unwilling to alter the agreement upon lease renewal which is coming up in 3 months so I contacted a new PM company who I want to take over.

The owner is aware of my intent to sublease and has also given permission for the alterations I want to make to the suite.Anything else I should be considering?

If you change your mind or add something to the project that alters the timeline of that plan, it will cost you money.How can you minimize these occurrences?

Appraisals and FMV do matter for this allocation, and cost segregation can alter this allocation, too.3.

Does anybody have advice on how to properly adjust our offer price to reflect the risk associated with these unpermitted alterations?

Consider the alternative - if you walk in and say 'I'd like to use this zoned commercial building for a store and do some mild alterations' and they say 'I perceive no possible issues with that whatsoever' - couldn't you come back around and blame them later?

She’s also changed the locks on her door and altered the premises.

Or do I have a legal right to un-alter the premises?

The purchase price is typically not altered by the commission fee.