Large servicers don't charge people for modifications, but I guess since it's private you may be able to, but I'd do some research on that and any legalities. 

The lease is typed out but the modification are in ink.

Considering a part of the BRRRR strategy with some modifications.

Is the property in need of any repairs or modifications to pass city or county inspections? 

It's going to need some modifications.

She stopped the foreclosure proceeding and the bank rescheduled the sale and started a loan modification (or whatever thats what she told me).

As long as you do that (allow them the ability to have them installed, and don't "prohibit" the modification) then you have made a reasonable accommodation and are ok as far as the ADA/fair housing goes.Obviously you really should read the appropriate portion of the act yourself, and if you have any doubts or questions seek appropriate legal counsel.

Many accounts had immediate re-default post modification.  

If you don't get the ZBA approval, you can keep trying and making modifications to your plans.

Have a local attorney review your modifications, especially on the first one.