I would try as gently as possible to walk the manager through the missing funds and try to reconcile those, then part ways as soon as possible.I would also HIGHLY recommend changing the way you operate with regards to taxes and insurance payments. 

The basement of this property has wood paneling covering the foundation and there is very evident signs of moisture and mold. 

Third thought was moisture but if there was a moisture issue I would assume it would be all over not just that one spot. 

Use a moisture termite inspector who will make you a diagram of what needs to be done do your contractor can do the work.

Not true the ceiling needed to be patched and painted, carpet replaced due to all the stains and mold, the bathroom vanity replaced from moisture damage and the bill paid for the drying company.

I think that bring out another contractor might be helpful but also finding someone with a moisture meter to help identify it might be helpful.

In Ohio there is almost always problems with leaking in the basements or moisture build up.

I try to gently let tenants know that each fall/winter, in an really old graystone, there are probably going to be some occasional incursions.

There's a moisture meter that costs $40. 

The low volume / quiet fans have been useless for us, they just do not clear out the moisture.