I have an 06 XL 1200 that just started choking out

This could be a variety of issue's from over choking, to bad fuel. Make sure your not leaving the choke on to long, as this can foul the plugs. Bad fuel could cause this, as water or other contaminents get into the float bowl and don't affect the enrichment ports due to fuel bypassing the float bowl. This would lead to the bike running worse as the enrichment knob is pushed back in. Last but not lease, could also be an electrical related issue due to the bike warming up and causing a short or open as stuff expands. I would change your plugs, then drain the float bowl into a clear glass jar to examine contents. if fuel and spark seems ok, you will have to look at electrical. plug wires, crank shaft position sensor, coil. It may take someone with the tools to test these components in order to diagnose the issue. If you see that the tach (if you have one) or lights in your display's flicker, it could also be battery related. loose ground. Many possibilities.