I am using Quicken Loans and I have submitted all the required documents and the QL agent is telling me to hand sign some application and e-sign some paperworks.

Look at the buyers personal financial statement with liquidity and net worth.Step 2.

The seller had poor records or something weird where the income on the Schedule E didn't work for the bank.

The Bigger Pocket's Allison person send me an e-mail with an investor post that talked about how IRR is more important to an investor than NOI or the cap rate, but nowhere in the article did it explain what IRR is.

If there is no way you can move in within 60 days (because none of the leases expire during that time) the bank will not give you the loan, as it would be mortgage fraud.  

At the moment I am not liquid enough to put 25% down of the project LTC loan.

I have a seller that wants to sell cash but the tenants lease expires in 6 months!

After this point you would use the schedule E income that shows the rental income that you claim. 

If they don't want to then just say N E X T!!

I'm viewing it as more of an investment, so don't want to tie up too much of my liquid capital in a down payment.