Sorry I did not see this earlier, but I think you went the right way.
The R value of the floor the way I did it with 1 inch polyiso, 1/4 inch plywood, and vinyl floor is about R7.5.
If you go down to the 5/8 ths wood plus Vinyl with no added insulation the R value would be down to R2.2.
For our van insulation levels, and assuuming 32F outside temp, this would increase the heat loss for the whole van from 2410 BTU/hr to 3163 BTU/hr -- about a 30 % increase. Quite a bit.
If you left the 5/8 ths floor in and added 3/4 inch polyiso plus 1/4 plywood plus vinyl, the R value would be about R6.7 -- so, not much reduction from the R7.5 the way I did it.
The heat loss at 32F outside would go from 2410 to 2450 BTU/hr -- only a 2% increase in heat loss. You could even use half inch polyiso instead of 3/4 if every inch counts -- This would give you R 5.2 and increase heat loss at 32F from 2410 to 2550 BTU/hr, or 6% increase.
I guess the main message is that you probably want to get some insulation in the floor stackup, but it does not have to be the full 1 inch thick to do a pretty good job.
I guess if it were me, I'd have a hard time ripping out that nice factory wood floor to gain only a few percent on heat loss?
This page has a link to my van heat loss spreadsheet -- you can download it and play around with different combinations: http://www.buildagreenrv.com/design-...n-conversions/