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HKSkully said:
Do they come loaded with different base MAP configurations already installed in the updated files?

Say for instance for my 06 Ultra's configuation of Stage 2 1550 big bores with SE flat tops and 203 mid torque cams? Or will it have a file of one of the MAPs in its file program that would, say for instance, be close enough for me to finish programming with the SERT?

HKS: Here's one of the maps from the SERT's current offerings:

Calibration # 29: 2006 Touring Exhaust (includes FLSTSCI)
Configuration: 1550 Stage 2
File Name: 141MJ013-A0.MT6
• SE Air Cleaner and Breather Kit P/N 29440-99C
• SE 1550 Big Bore Cylinders P/N 16546-99 or 16549-99
• SE 1550 Flat Top Pistons P/N 22851-99A
• SE 203 Cams P/N 25937-99B
• SE Performance Touring Mufflers P/N 65115-98B or 65116-98A
This would work to get you started; but as darkknight stated you'll want to eventually get the bike dyno tuned by a competent SERT Tuning facility.

If you don't feel comfortable using one of the included maps, which by the way are usually configured to run on the lean side, there's the option of getting a custom map from www.hdmaps.com

Good luck!

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