If you're serious about installing an auto headunit, here are the bare minimums.
#1- go for a "marine" headunit. They makes the same style units specifically for boats, with circuit boards that help prevent corrosion. They still aren't waterproof, but they do make enclosures that are, and many have waterproof wired remote controls.
#2- carefully evaluate the power usage of the head unit, as the FJR doesn't have much room to spare. Since you'll be running through an autocomm, finding a unit with only preamp outputs, no internal power amp, will be best. These are typically more expensive/higher quality units, and may not even be available in marine versions.
#3- you defiantly want a pre-amp output for going to the autocomm, but most head units will have these now adays.
#4- due to the head unit requiring constant power to store radio addresses, clock, settings, etc, your tankbang will need to be a semi-permanent install. (or wherever you choose to mount the radio) You'll need to run two +12v power lines to the radio, one constant and one switched with ignition. Keep an eye on how charged the battery stays.
past that it should be pretty straight forward, but if you have any questions...