1. This watermelon came with a Thundermax ECM. The intake and exhaust are stock. It has the oxygen sensors. I am definitely going to change exhausts. I prefer true duals, but would like some input on true duals vs. 2 into 1, pros and cons of each and brand recommendations.
2. The stock intake, it is considered a Stage 1? Is there a better intake for it?
3. Will this Thundermax have to be re-mapped for these changes?
Here is my input on your questions....
1. I too prefer true duals, but have come to like the D&D Fatcat 2-n-1 more and more. It will provide you better all around performance, and it has the option of having a "ghost" pipe on the left side which will give the appearance of a true dual. Not sure if I would get the "ghost" pipe if I were to go that way as I'm getting more used to the single pipe look on a bagger. In regards to true duals I like the look and sound of the Rinehart's (have these). As you stated many have these pipes but that didn't deter me from getting them.
2. If you look behind the A/C and it still has the black plastic/rubber backplate then it's going to be the stock (not stage 1) intake. If you are going to change the pipes you'll need (should) to change this also. Look here -
"Roll Your Own" SE Air Cleaner for a great alternative (chrome) for this mod.
3. I believe there are different downloads for different modifications available for Thundermax ECM's. Check this site -
Thundermax and you'll find the software available for download. There may be a map available for the A/C and pipes you are intending to install on your bike. If there is a map available (for the mods you've made) it is supposed to get you close and then the auto-tune is supposed to adjust to your specific bike.

Ride Safe,
Fired00d