The turn signals flicker. Mostly the front but sometimes the rear. Is that the Aux port?
No, it should be wired that the M-UNIT is powering those from their respective TURN L and TURN R circuits.
You never said, but I'm going to assume that you used "stock" or "stock-ish" style controls at the handlebars? If so, you likely still have a ground issue.
Maybe. Do the lights flicker constantly, or only when they are illuminated? Is it just the indicators, or do other lights do this?
If its only the indicators, and only when active, then its down to a poor ground. The M-UNIT has a built in flasher relay. It also allows you to program the indicators with a % of illumination for using indicators as running lights. And, if that weren't enough things to consider, programming the M-UNIT for which handlebar controls you have also matters.
If you can snap a picture of the L and R handlebar control units, and the indicators (are they stock or aftermarket? Are they incandescent bulbs or LED?) that would help.
Actually, some complete pictures of your bike would be nice too!