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Do you have the option of putting your license plate on the account for the EZ pass? In Illinois, I only have one transponder that is in my car but have my bike and wifes car on the account. It reads the plate as I go through the tolls and takes money from my account, dont have to worry about carrying it on the bike.
Windshield pouch has always worked fine for me. When I had a RG I kept it in one of the fairing storage compartments. Others have mounted them on the inside of the fairing, lid of the tour pak and lid of a saddlebag with no issues. Depends on the strength of your transponder and the strength of the reader at the toll plaza.