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So last night I put my passenger side glass in (yay), so I went for a test drive, I noticed that every 20 seconds or so the MPG reading lights would flash "SYS" twice then return to normal. I didn't notice it on the way to work this morning, nor could I find anything in the shop manual under section 8, nor did any of the warning lights come on...
It will flash SYS when there is a CCM problem detected. Which can be caused by all sorts of things: low battery voltage, removal of Bose system, etc. If it is not doing it right now I would not really worry about it, the problem must have corrected itself.
I'm betting you didn't disconnect the battery while you were working on the door - interior lights on and maybe radio too? If so, your battery may have discharged enough to cause the SYS light to flash. It may have been weak to start with.
Mine cleared up till we were about to hit the FLA Keys. Then it died at the gas pumps. Walmart was only 1/4 mile away. If your battery is over 4 years old get a new one. Cheap insurance.