In our old coach, we replaced the carpet with sheet vinyl flooring and encountered similar problems. In our case, the sub-flooring was just at different levels, it was solid and not flexing when walked on.
We used a cement-based underlayment/leveler (I believe it was Armstrong brand S-183, it came in a 10 pound bag from Home Depot, you mixed it with water to use) to even out the floor.
We also found that where we did not use the leveler we had print-through from the old flooring (i.e. the embossing from the old flooring showed through)
. Fortunately we had used it in all the places that showed, only the storage areas had the problem
. Note there are better products for this use, we used the S-183 because we had it.
We used the coach for 3 years after the installation and had no trouble with the new floor.
Hope this helps!
Stewart