Would we be able to pocket the buyer commission to remedy the final sales price or closing costs?

I had a water leak at a property that required remediation.

Can I charge him money before these things are remedied? 

Unless the professional you called is qualified* to say the tree was an immediate hazard and given the situation, it could not wait to be remediated because property and/or life was in jeopardy, you're going to be on the hook for the removal and could also be on the hook for the replacement of the tree + additional damages. 

Depending on the auction terms it could be that result plus the forfeiture of your deposit, or perhaps the trustee/auction company must elect one remedy vs. the other.

most work is flooring, remediating the basement, paint and updating one bathroom along with siding repairs/likely window replacement and massive landscaping and  concrete work I like doing.

Hopefully you can get remedy quickly. 

Would you ask your surgeon to reduce his price before doing open heart surgery?

Legal remedies can get costly.

It tested low: Highest levels are .3, well below the 1.5 legal limit for contamination.However, it’s been suggested that I still might want to hire a remediation company to do HEPA-vac + wet wipe throughout the home.