There were no clean upslisted, what else should I look for? 

We spent several thousand on the cleaning, touch-up paint, and repairs.

Bathrooms are cleaned weekly by professionals and the house is treated for pests monthly.

Seems to be so basic but lacking in an alarming number of people:Show up on time, or call if you are running late.Answer your phone.If I try to contact you via phone or email, I expect a response within 24 hours barring an emergency.Pick up/clean up after yourself and make sure the subs do too.Drives me crazy to see cigarette stubs all over the place.

I might get trash cleaned out or have the yard mowed, but that's about it.  

Have a contractor coming to clean this up and he wants 6 hours of labor for it. 

Any recommendations on the deposit/cleaning topic?

Offer to not require an increased deposit (you should get their old deposit from the seller held in an escrow for you) if they leave the unit clean, otherwise, you will deduct cleaning from their old deposit and require them to furnish a new deposit with the new lease.I would say that I am not a lawyer nor do I offer legal advice, I would check with an attorney who specializes in rental law to determine your rights and responsibilities, at the end of the day, you sign with a tenant in the unit, you own their lease as it is written.

Unit to be broom clean.

Thanks for the link @Chris T. the 3 times income to rent rate and clean credit score may help... i think more so in the more expensive markets, but in lower income housing... i think you'll be hard pressed to find an applicant with clean credit or income that can back your justification on denying the ex-con..?