Here is an archived copy of the Invitrogen 3-insert multisite Gateway manual, version D, 3-07-07. We originally had a live link to the Invitrogen site, but after this link broke it seemed easier to hard-archive a copy.
Invitrogen Manual Version D (link updated August 2017)
Note that Invitrogen seems to be continually tinkering with both att sequences and nomenclature, with no documentation of the changes. For instance, the attB2 and attB2R primers switch names between version D and version E. The Tol2kit was originally constructed based on the version C manual; version D seems to be very similar with minor improvements to protocols. We have stuck with the version C/D nomenclature, rather than trying to keep up to date with their changes. Note however that the Vector NTI software distributed by Invitrogen now uses the version E nomenclature.
Presumably att sites from different generations of the kits are still functionally compatible.