Because I keep my DLX on a concrete floor now, instead of a rug, I noticed a small puddle of water beneath where the mufflers meet the headers. I looked and noticed that there was a drain hole and assumed that it was to drain condensation from the exhaust, okay that's good. A few days later, after an all day ride the previous day, I stood the bike up off its side stand and I got a large rusty puddle from the right side only. Okay, that's not good. I concluded that this bike needed to stay on its center stand when being garaged so that the exhaust can drain properly.

Interesting. As a suggestion; have you thought about fogging the exhaust with WD40 when you put the bike up for winter?
Thats a possibility, are any other DLX owners concerned about this ?
Functions of catalytic converter:
Reduction of nitrogen oxides into elemental nitrogen and oxygen:
NOx→Nx+Ox
Oxidation of carbon monoxide to carbon dioxide:
CO+O2→CO2
Oxidation of hydrocarbons into carbon dioxide and water:
CxH4x+2xO2→xCO2+2xH2O
I think I'm having an acid flashback to chemistry class in the '70s.

My DLX also often leaves rusty puddles on the floor
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My concern is not that there is water coming out, but that there is rusty water coming out.