IIRC, Dobeck doesn't offer a system compatible with the MM EFI system which is is fairly primitive and was replaced in 2002 by the Delphi system. That early MM setup uses a batch fire, speed-density system with a very basic ECM and hard-coded fuel/spark maps, so not every modern tuner works with it.
Best bet is the Dynojet Power Commander III USB with is a "piggy back" tuner that "tricks" the MM ECM; it does not flash the ECM. It would take a shop with a dyno and the older PCIII software to flash the ECM.
Most owners of the early Harleys with the MM EFI system go one of two routes:
1. ECM Replacement Conversions like the Daytona Twin Tec TC88A/TC88 with MM adapter harness or the Thundermax EFI which is primarily for designed for Delphi EFI but there are kits/adapters for the MM bikes but some sensors have to be replaced..
2. Carb Conversion with kits from S&S or Drag Specialties are still available. Many revert to this conversion to do away with EFI altogether. There are many posts on other forums from owners that have converted to carb with OEM parts and aftermarket ignition module and carburetor.
If just replacing exhaust and intake, basically a Stage I upgrade, a re-tune may not be required; don't have personal experience. For the OPs situation, a used PCII USB for MM EFI is the easiest route but they are more difficult to find. They do show up on Ebay fairly regularly, just make sure it is the MM version, Delphi version won't work. For full control, the Daytona Twin Tec or Thundermax is the better long term solution but more expensive and does require some wiring changes and wideband O2 sensors in the exhaust.
Or, if "rideability" is not significantly affected by the Stage I upgrade, just ride.