Thank you for your reply. We ended up having the dealer take a look at it and they said it was normal. The weight of the dinette may be the reason why it is a noticeable difference now. They said to just try to avoid standing on it.
it does appear to be sealing on the outside and nothing visually looks wrong so keeping fingers crossed that is all there is. Love our modifications though so it was defiantly worth it. We also cut down the top bunk to bring a little head room and light to the lower bunk. It was tight and dark.