I have a 2004 883 sportster that I converted to a 1200 10.1, I also changed the pipes from screaming eagles 2 in 2 to new pipes FatCats 2 in 1. The card was rejeted.
As Terp is basically implying, you paid good money to get the engine beefed up, but not dyno tuning it for maximum performance & response would just be a waste.
Get a Daytona Twin Tech ignition module and talk to Turbota on XLforum.net. He makes custom MAPS for Sportsters using the TC88A that allow them to run a lot better than just using the settings on the module itself.
Then get it dynoed. I went from 71 HP to 78HP with the TC88 install and using the settings. I am in the process of getting the custom MAP installed on my module. This should give me a few for horses.