Quality isn't as good and they charge more.  

What would be an appropriate charge for water passthrough?

Not all properties have an HOA/maintenance/common charge fees.

If the unit is damaged because the leak was allowed to continue, I would charge the tenant for the additional repairs required.If tenants have such obvious lease violations, there is a high risk of additional problems down the road.

As an aside: Contact your credit card company and tell them what happened and most likely you'll get a 'charge back'.

Otherwise, I was going to look for a bank loan and try to get something that charges me as I draw  (vs getting one big loan all at once) and slightly lower interest.

There has to be some form of a written agreement on who gets what of the profit, who's in charge of maintenance, what happens when a partner wants out, who's on the loan/title... etc  I find it hard to believe that this person wouldn't just take this deal and run with it on their own since they are funding everything with their money and I won't be giving a dime.

I charge my tenants an $80 flat fee for water and trash. 

That's considered "neglect" or "abuse" and I would seriously consider charging the tenant for at least a portion of the repair.In the future, you should only renew after a complete review of the tenant's payment history, communication, care of the home, etc.

Also there is a laundry room that he currently doesn’t charge for, I’ll be adding coin op laundry and charging a small amount.