As a tip, I find that one of those inline 8P8C female to female adapters is great for snapping on the end of network cables for removing them (from a mess) to keep the retension tabs from being snapped off. Of course, it's even better if the cable was manufactured with one of those boots which serves the same purpose.
A few questions, if you don't mind...
Removing everything then building it back up means more downtime (I would think) because (individual) things are down as cables are removed, the whole thing is completely down at approx. the midpoint, and it's not completely back online until you're done. Is there a rationale behind not replacing one cable at a time? It's a different problem of course, but one at a time is the way I'd replace spark plug wires and/or spark plugs so that there is very little chance of getting the wrong firing order. Likewise, if cables were replaced one at a time, I'd think this would be at least somewhat less error-prone because there will be a cable end hanging there somewhere around each socket, and it's at least possible to test each reconnection individually, instead of getting to the end and wondering "holy crap! It doesn't (completely) work, so where in that whole exercise did I frak up?"
What do you think about custom making at least some of the connections with a spool of cable and connectors (for wire anyway, probably not as practical as optical)? That way, they're exact length with no or only moderate excess (I always leave a little slack if I can). The potential tradeoffs of course are reliability, as premanufactured cables are quite usually tested and presumed good, plus it takes (usually nontrivial) time to put the connectors on.