Let's start with this piece:
Roughly $840 per month PITI. A positive cash flow of $1160 isn't too bad a deal?
$1160 would be very nice for cash flow. You won't even come close to that. Go to the Rental Property forum and read the sticky threads about expenses. This statement is based on the number one big lie told to new RE investors: "cash flow = rent - PITI". IT DOES NOT!!! You say your a new investor. Please, please don't believe this lie. Its just not true. Read those posts and you'll understand the reality of rentals much better.
In your first post you say the property will be purchased by you from your LLC using owner financing for 100% of its current value. Assuming you pay the closing costs for that loan, about $5000, I'd estimate, out of the cash you have, you are correct that the P&I would be only about $640. With total rent of $2000, ALL expenses, vacancies, and capital items of about $1000, you're left with $1000 in NOI. That gives you real cash flow of $360 a month. For a duplex, that's excellent. Not the unrealistic $1160 you're thinking, but a great deal nevertheless.
The listing agents comission is paid by the seller, not the buyer. If you're buying this from a bank, the bank is paying that comiission out of the $30K sales price. This should not appear on your side of the transaction. Even if you pay the full 6% out of your money, that's $1800. If you do this, be sure its not on the sellers' transaction, too. Not saying this might not be what's being done, but this would be a very unusual way to handle the commission.
If there is a commission on the sale between the LLC and you, then I call BS. There should absolutely be no commission on that sale. If someone's slipping a commission in on that second transaction, then they are blatantly ripping you off. Please tell me that's not happening.
If I understand correctly, your getting about $42,000 from the transaction funder. $3,100 for the transaction funding is about 7.5% of this amount. Thats a very high percentage. But, perhaps there's some big fee plus a percentage that makes this high for the small amount.
I'm not sure what the note buyer finder's fee is 1% of, so I'll assume its 1% of the $95K face value or $950.
I'd estimate closing costs, even for two transactions, to be only $3000 at the most.
I'm only coming up with $8,850 in fees, not $12,000
Transaction funder: $3,100
Note Finder: $950
Commission: $1,800 (6% of $30K purchase price)
Closing costs: $3,000
Total $8,850.
Where's the other $4K?
So, overall you get a $95K loan. The note buyer pays $80,750 for that note. You pay off the $30K purchase plus the $12K in other stuff and you have about $38,750.
You spend $12K on renovations, $5000 to refinance, and you're left with about $21,750. There will be interest payments to your private lender. It would be safer to assume it may take a year to get the refi completed, though I would hope you could make it happen faster than that.
Speaking of the refi, you will need to be sure you qualify for that. You'll need enough income to cover the new note and all your existing obligations. You may or may not be allowed to include the rental income. Fannie Mae guidelines require it be on two tax returns before it can be counted. Other lenders can be more flexible. The lending environment is ugly. I'm in the middle of a refi right now, and it changes day by day.
The HVCC guidelines are yet another new wrinkle and I'm hearing of some dreadful appraisals. Please be extremely conservative with your values. If you want to refi the $95K, you'll need every penny of that $125K valuation. Really, more like $127K. You'll have no control of the comps the appraiser uses, so be sure the worst comps support that value, not the better ones.
I'll ask for the third time if you've independently verified the value and the rents. At best, sellers always slant their story by using the best comps they can find. That's not what the appraiser will use for the refi.
So, yes, this seems like quite a good deal, assuming the value and the rents are correct. I remain concerned that there is a lot of money seemingly disappearing off the table. You say these fees are reasonable. I don't see it. But perhaps the end result makes it acceptable.