I am looking for suggestions on how to structure a partnership (short term) that will benefit him but allow me to be dissolve our partnership after a couple years as he isn't interested in long term holds. 

You can simply request a separate check for the $100 increase to bring the total deposit in line with the new rent amount.

Everyone was just rolling with the punches there for a couple years. 

These two concepts are separate from each other.

I know a couple people that does this, let me know if you need me to connect you. 

and even if you aren't going to do an inspection, can you walk it with a couple contractors?

I proposed the question if the separation of funds was for asset protection.  

(I actually laughed when I first learned this.)10% property management fee (With separate charges for new leases, repair management, and rent collection—what exactly does this cover?)

What is the best way that you have found to tell them that you need labor & materials separate, so at tax time you can send them a 1099 for labor?

Find a good lawyer you can make a relationship with to have in your back pocket should you need to sue, use strong contracts, use work tracking apps like busybusy, always have a couple of different contractors on speed dial so you can fire them and replace them immediately. you've got to be bullish, have strong goals in mind.