After the meeting, I said I will move forward and paid the deposit of $1000.

I'm just more familiar with people quoting gross rents and typically assume the cleaning fees are being paid by guests. 

For example, I often see Buyers purchase property thinking there is a $1,000 deposit but then the tenant claims it was $2,000 because they paid the last month's rent.

You should speak to your cpa but if multiple people are paying it then I believe it can be separated as long as it does not exceed the amounts paid and it must be legit

My partner also wants reimbursement of the funds paid for the home inspection.

No but if you paid for those items you could get copies of them and use them for a private lender who may be able to give you a loan.

I had been with them for 18 years and paid off mortgages, never missed a payment, never had a problem, etc.

For example, I used a HML (hard money lender) to fund the acquisition of a property in Indiana I purchased off-market from someone in foreclosure, but paid for the rehab with my own cash.

I set up the entities using diff companies and paid about $1000 for all three (I got minimal boilerplate operating agreements).

All this can render a pre nup irrelevant in community property states.