You may not have known your battery or charging system was weak, but a good lesson for anyone reading this post is to verify the health of the battery or charging system prior to installing a tune.
The very first paragraph on the SCT tuners guide is : STOP. Check all electronic systems.....
You are lucky in that the battery did not completely die during the tune install/reload. This could have messed up the ECU, causing a call to customer support (good luck with that on weekends), or a trip on a flatbed to your local Ford dealership for a stock ECU reflash (and out of your pocket expense).
It is better to keep your mouth closed and let people think you are a fool than to open it and remove all doubt.