So I would be refinancing the main house at 5.0% fixed for 30 years for a $490,000 loan amount (to make it conforming), and the investment property at 5.375% fixed for 30 years for a $110,000 loan amount.There will be about $17,000 total in closing costs for both loans, due to 1% origination fees on both loans and high closing costs in my state.I just don't know if its worth it.

If you don't have your limit of 30 year conforming mortgages, I would put one on the single duplex. 30 year fixed mortgages in the 4-5% range can't be beat.6 units on one lot and 8 units you're probably going to need a commercial bank loan with 20 year am/5yr fixed slightly higher interest rate.But... there's also the convenience factor to consider.

Further, the lower level unit wasn't in conformance with current egress code requirements.

One of the problems here, which may be similar in other places, is that new construction has to conform to newer setback regulations & the lots just aren't big enough.

That being said, you are certainly in luck because the VA loan is available to you in Hawaii and you may even have higher 0% borrowing limits because the borrowing cap is location specific and while most places have it set at the typically Fanny Mae conforming loan amount of 417k certain high value markets (like DC, NYC, HI etc) have a higher cap.

But you can close non conforming loan products like DSCR, bank statement loans, or asset based loans in an LLC. 

The 10 loans is not a “hard and fast rule”, those are limits set by Fannie and Freddie and since most lenders just sell off their loans to those two outfits, they need to make sure the loans conform to their rules.To get past the 10, you’ll need to find a portfolio lender, which means they don’t sell off their loans to Fannie and Freddie, the keep them in house.

Mortgage lenders tend to broker mostly conforming loans, but banks have in-house products that can be very interesting.  

FHA Basic standard mortgage limits are:Single - $275,665Duplex - $352,950Triplex - $426,625Fourplex - $530,150Fannie Mae/Freddie Mac standard mortgage limits are:1 unit - $424,1002 unit- $543,0003 unit - $656,3504 unit - $815,650Conforming FHA Basic High Cost area limits are:Single - $636,150Duplex - $814,500Triplex - $984,425Fourplex - $1,223,475Maximum Conforming limits are below (If Your Area Qualifies, For Specialty Financing);Honolulu; Kalawao, Maui; Kauai;1 unit - $721,150 1 unit - $657,800 1 unit - $713,0002 unit - $723,050 2 unit - $842,100 2 unit - $912,7503 unit - $1,115,800 3 unit - $1,017,900 3 unit - $1,103,3504 unit - $1,386,650 4 unit - $1,265,000 4 unit - $1,371,150FHA Loan Limit Look UpVA / Conforming / Fannie Mae / Freddie Mac Loan Limit Look Up

The property has two conforming bedrooms (egress windows) and 2 bath in the basement.