I have what I believe is the latest SERT--got it last month--Version 4.5.2. The only '06 model CVO map is for the FLHTCUSE (141MP002)--there is no equivalent SEFB map, like there was for the '05 SEFB, unfortunately. There are a couple of maps for '06 "Super High Output" motors, which one could try, but, of course, we're talking very different cams, heads, etc.
GC, I thought about this question over the weekend for folks who have an '06 SEU and want the equivalent of the '05 SEFB map for their bike. I was specifically thinking of FR8TRN, because I know he just put on V&H Dresser Duals and is running a SERT now on his SEU.
I guess if I were in that position (of owning an '06 SEU), I might spend some time trying to understand the differences between the '05 SEEG (127HX022) and '06 SEU (141MP002) maps, table by table, and then try to superimpose those difference onto the '05 SEFB map (127MK004). Kind of an extrapolation of the year-to-year changes which you then use to create a "new" '06 SEFB map. That map could then be further modified as described by Syclone in the link attached above. Obviously this is very imprecise science at best, but it might get you to an understanding how the SERT maps change because of year-over-year model changes, and then use that understanding to create a new SEFB map from the '05 SEFB version (127MK004). It might at least provide a closer starting point.
Anyway, that's the best I could come up with.