Yes it does have a flasher mode. Humminbird does not list a ice ducer that is compatable with the 798. You may want to call them to find out for sure though.
There is no problem using a SI or DI unit with iPilot. The problem that can occur is that the DI and SI will not work if you are using the universal sonar. You will need to mount an external transducer on the trolling motor for those functions.
The transom mounts are good and as long as they are not abused you should not have any problems when they are installed correctly.
There is a factory reset in the menu on the units and there is likely a hard reset too that Humminbird could provide you. These are generally a key sequence when powering on. Its extremely rare a unit has problems during an update when the instructions on how to update are followed.
-Lawren
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