The only way it can blow cool air is the burner goes out. That's not a motor issue, so you must have messed up something when doing the swap. Possibilities are anything that interferes with the combustion air intake or exhaust output, the Hi-Limit switch, burner is overheating, or gas pressure drops too low. One place I would look right away is the gasket that separates the circulation air path from the combustion/exhaust path. If air leaks between the two, it often interferes with combustion, plus it is potentially dangerous (exhaust fumes get inside the RV).
Take a look at my Furnace Troubleshooting Guide in the forum library at http://www.rvforum.net/miscfiles/Furnace_Trouble-2.pdf