I haven't had time to sit and read through all six pages here, but a few things I noted and wanted to drop some thoughts on, so apologies if they've already been hashed to death;
re; Transwarp failing or not.
I personally like to stick with the 'common' theory that it didn't quite pan out, but on the flip side to reinforce the fellow who mentioned the Ent-A's Okudagrams mentioning Transwarp, the old Mr. Scott's Guide to the Enterprise mentions in it's last chapter about the Ent-A (...which was appearently named "Ti-Ho" previously -shudder-) that the -A had Transwarp as well.
re; Length of refit
Rather than attempting to come to some conclusion on the length of one large refit, have you thought about most of the changes not being the result of one refit, but several? Excelsior in many ways can compare to Battleship North Carolina; North Carolina was the first Battleship built in almost 20 years, and incorporated a lot of new experimental technology. As a result, her shakedown period was considerably longer than the following Battleships of the period, and she gained the nickname of "Showboat" because she was constantly shuttling back and forth between sea trials and yard periods. Considering Excelsior is the pathfinder for all manner of new technologies, it's more likely that her first few years in service were similarly spent working out all the kinks, with technology that didn't pan out being removed as needed, and other changes being done similarly. Certaintly there isn't as much major structural changes between ST3 and ST6 compared to the TOS and TMP Enterprise to warrant a single refit lasting more than a few months, if that long. However, having the ship going through ongoing testing and parts swapping for those years is definately plausible, especially if the class concept goes through some kind of role change.
I am curious, since I haven't seen any mention of it thus far, but is there any link between the tech manual you're writing, and the "Space Control Ship" history that was in the Ships of the Starfleet book that came out in the 90s?