I have the same 5500 gen set. I moved the exhaust to other side just like you did. Unfortunately I did not get the installation instructions, but I did read in the operation manual a warning about back pressure causing overheat of unit.
You also need to make sure the pipe has enough down angle to allow the water to run out.
Maybe they are just protecting themselves, but it is something you might want to check on.
Dealer installed mine and I was not happy with the installation, left huge gaps in the floor. I sealed it all up with gorilla tape and seems to work and doesn't look bad. Still has the correct airflow for cooling but keeps the water out of the storage compartment.
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2007 Chevy 3500 Dually Duramax Allison
2013 Keystone Alpine 3555rl, Onan 5500, Directv Dish
2004 Everest 364Q
2005 Larado Bunk House TT
2004 Komfort TT
1973 Kenskill TT