A year after I bought our 2004 Rockwood new, I wanted to install a cargo door in the rear storage compartment. The factory had a small access door that was WAY too small for the storage area size. The next year, Rockwood realized this and fixed it with a larger door! I talked to the dealer to see if I could order the larger door from Rockwood. He checked and said yes, for $350 (for just the part)!!.
I went on ebay and found a NEW door someone was selling. He had a batch of never-used doors from a door/window manufacturer that were mistakenly made slightly off-size. I paid $10 for the door (plus about $10 shipping), installed it, and it has worked perfectly since.
Check ebay under RV parts and you may find a pair of windows far cheaper than getting custom ones made. You have a range of sizes that would work since there is no opening now. This gives you some flexibility in the window size.
Steve