I may be wrong.... But.... I believe you are doing more than needs to be done. I changed from the stock Boxster cluster on my 2001 Boxster S to a 2003 996 cluster. I also have the green, blue and grey connector on both my Cluster and the 996 donor. The only change I made to the 996 cluster was to send it in to
ODO-PRO.COM - Odo-Pro.com - The Digital Odometer Professionals and have the odometer changed to my Boxster's for $89.00.
I have read post that talked about the need to make changes using the eeprom on the new 996 cluster if you have a 2003 or 2004 Boxster with a MOST system. We don't. If your donor 996 cluster comes from a coupe, a turbo, a C4, or if the PSM system was or wasn't an option on the two cars.
You may want to install the 996 cluster and see where you are.
Others may have more information on this, but for me it was pretty much a plug and play mod. I have PSM in my Boxster and the donor 996 didn't. I need a PST-2 or PIWIS (or a friend that has one) to activate those lights. That is the same tool I believe you use to reset the 996 cluster to a convertable from a couple and to a C2 from a C4.
Good luck and keep us posted.