Now, the pending refit.... Are the issues with the core or the nacelles or both?
One fan-version of the "failure" that I worked on had the problem confined to the nacelles, what took so long refit wise was the construction standard warp nacelles in that size, essentially the delay was retooling the assembly line to make "standard" warp coils instead of "transwarp" coils. The revolutionary "warp-core" design stayed the same, and allowed the refit Excelsior with it's "Extra Beefy Standard Warp Drive" to actually set some of the promised speed and endurance records that Transwarp failed to achieve.
In a nutshell, both. The idea (so far) is that the engines are basically too powerful for the ship - while they do reach incredible speeds, the idea of a 'jump' drive as initially envisioned proved impossible mostly because the high-level warp fields that the ship was reaching started to 'melt' the structural integrity. So, Starfleet has to redesign a new, conventional warp core (using what they learned to build the first transwarp one as their guide) as well as the gargantuan warp coils you describe, that isn't technically as powerful as the first one, but also not prone to the same 'overpowering' problems.
Thus, we have the prototypical almost-there model of the TNG warp setup. In my reckonings (and a future chapter), the Ambassador
ends up being the 'real' modern engine design and that's why the adaptation of the recalibrated warp scale coincides roughly with its construction and launch.
So basically the transwarp project technically fails to create a 'jump drive' but ends up successfully creating a newer, faster, better warp drive.
That's just one possible idea... another idea had them using "transwarp coils" reverse engineered from Borg technology and while it worked as promised, it attracted the attention of a Borg Sphere which was intercepted in the Tomed system by a joint Federation/Romulan taskforce. The Federation was forced to abandon that particular mode of Transwarp because it seemed to attract boogymen.
That... that's supposed to be classified.
Seriously though, amazing work so far. Can't wait for the next installment.
I shall probably post the next later on today after giving everyone interested a chance to respond to this rather long chapter. Once all the history stuff is outta the way, we can get to the actual nuts and bolts.