I know it's not helpful to think about now that you're 40% done, but we just put foam underlayment on top of the original floor and covered it with luan to stick self adhesive tiles to. Other places of our floor have original floor, foam underlayment, and then laminate wood floor. We removed the metal strips on the sides of the aisle, but left the grooved aisle floor. Even with the 1/8 inch grooves it's almost completely unnoticeable because the foam conformed to the spaces.
My build thread:http://www.skoolie.net/forums/f11/build-thread-for-haulin-oats-and-goats-11237.html#post113500
A gal, a guy, three cats, two dogs, one rabbit, and one goat, traveling the country together.