These are a few short notes about what I've changed or adapted from both the Star Fleet Universe and the official Star Trek setting.
In my campaign, The Second Four Powers War never erupts into The General War. I assume that the Klingons decide not to open a third front in their war and make an effort to consolidate their gains in order to confront the Federation some time in the future. In all other ways, the official Star Fleet Universe timeline is valid up to the start of The Second Four Powers War in Y169.
Stardates have been a headache since they were first introduced. The Star Fleet Universe wisely avoids the whole subject and I would be happy to follow their example. However, one player feels that "it isn't Trek without stardates" (Dennis), so we worked out this system:
To make things a little easier, I worked out a quick table for the beginning stardate for each month:
The stardate system was instituted in Y153 (2254) which became year 0 for the system. The following year was 1000 and so on. The beginning campaign year of Y170 is 17000 in the stardate system. Thus 1 June 2281 (Y170) would be 17414 ... or something close to it.
So, where does Star Trek fit into the GPD/SFB Universe?
Hollywood has a way of taking true stories and actual events and making creative changes to make them more interesting to audiences. A character may be a fusion of two or more people, events that happened to one person are shifted to another, and other dramatic elements are added. Some examples include the movie Good Morning Vietnam and the TV series Ba Ba Black Sheep.
Applying this standard to Star Trek helps explain a lot of the inconsistencies in the series. Not every adventure directly involved the major characters; sometimes junior officers or enlisted personnel were the ones that got their shuttle lost in a nebula. Some events (such as the Federation-Klingon War) were compressed to fit into the show’s format.
Rather than going through all of the episodes and trying to rationalize the show with the GPD/SFB Universe, just assume that most of the events did happen, but not exactly the way it was depicted. In my version of the GPD/SFB Universe, the Enterprise had an historic mission, James Kirk was her captain, and the future version of Hollywood wrote its own version of those events.
Ignoring the inconsistencies in the SFB source material (TOS and TAS) is easy enough using the Hollywood explanation above. But the cross-series inconsistencies are much more difficult to explain (7 of 9’s origins and virtually the entire Enterprise plot line are two examples). The simplest and most reasonable theory is that each series took place in an alternate universe.