Unless you take the bike into a Dyno tuner, the best setup would be to load a map that has the closest setup to yours, there may or may not be one that is an exact match but ultimately the PC can be tuned for your particular setup and will net you the most from the bike. However, just loading an off-the-shelf map would still be a worth while as it will usually improve the throttle response a bit.
Yeah, I have the Delkevic, which are basically a knock off of the 99 headers (no cat, larger ID) with added sensor bungs. But I'm running the "stock 2001 with air filter" map at the moment and it is already a massive improvement over stock. Actually, just bypassing the sensors was a big improvement when cruising, but you can get by just fine with the the stock map or a map for air filter and slip on. I'll get a real map done at some point, but between the holidays and all the other work I just did I really haven't had time. It's still a huge improvement over the standard 00-01 fueling, so don't be afraid to just keep using it if you swap in the 98-99 pipes.
You could also call DynoJet and ask them for their recommendation. They might say "check the website, dude", but they also might be more helpful. Ciao,