The idea that something about the Excelsior or the transwarp drive failed to pan out is completely external to aired Star Trek. On the other hand, nothing is said or shown to establish that ships of the Excelsior design would have required transwarp to be feasible. Perhaps NX-2000 was just a random ship of that class diverted from the main production run for this rare propulsion experiment, while others were being completed with conventional engines for conventional purposes.
Both TNG and Voyager discuss the Borg having Transwarp drive in almost magical terms. I'd think it highly unlikely they'd so this if StarFleet had developed a working Transwarp system within living memory.
I would think that the innards would have to be redesigned to integrate a standard warp reactor vs. the transwarp drive variation.
That said whenever Voyager's on verge on getting transwarp drive it only ever seems to be half an hour's work to bolt it onto their existing systems - it can't be *that* incompatible.