I want this to be acceptable long term if I keep this method of financing. 

My humble advice to anyone attempting to do creative finance is:Creative finance is for experienced investors who have access to capital if anything goes wrong.Learn the lawsDon't use a contract "off the internet", laws vary by state and are also regulated on a federal levelLearn the financing techniques correctlyDon’t skip parts of the processDon’t ever do a “kitchen table” closingUse the proper deedAn attorney can help you with the legal work, but the rest you are on your ownYour guru will not bail you out“Investing” in someone else’s deal by providing a small 2nd loan so the “investor” can pay for “cash to the seller” and for “closing costs” so he can do the deal is a very bad planKnow what problems can ariseLearn the responses and solutions to problems before they are neededKnow everything there is to know about Title and what that meansKnow who a "protected class" individual isLearn the "back doors"Learn human natureUnderstand timelinesUnderstand regulation enforcement (some of these "mistakes" have a 10 year statue of limitations ( they can charge you 10 years AFTER you do the transaction) and carry hefty fines and possible imprisonmentThe court doesn't accept "I didn't know" for an answer"Know that the source of the lead plays a serious role in some states and federallyKnow how much of a "profit" pushes the boundaries to invite an investigationYou can be sued by the seller if you don’t do things correctlyYou are automatically at fault if an investigator or attorney or regulator gets involved.

The property itself should bring in revenue ( even if you choose not to live in one side) and generally a bank will accept a portion of that rental income into the calculation. 

Also, in a mainstream asset class like value-added multifamily, I see no reason to take a risk on a sponsor that doesn't have full real estate cycle experience or that lost anything more than a small amount of money (and prefer no money lost).

I offer an online payment portal to submit rent payments via ACH or CC - they "couldn't figure out how to use it" so I set us up to accept Zelle payments.

Still can be very beneficial for a new investor but personally I think not as good as a service as they had with their exclusive listings where they had inspections already done, rent rolls available, and you can complete the entire offer/acceptance via their platform rather than being handed off to an agent. 

How much is an acceptable fee for doing this? 

There are a lot of deals to be done with them if you can adapt to their process and accept they will be very slow. 

Don't accept ANY partial payments.

They then refused to accept responsibility for it.