The floor cylinders were probably part of the energizer room in "The Alternative Factor" in S1 since the dilithium crystals were in that room powering the ship.
I prefer to disagree on that. The crystals weren't powering the ship when they were in the energizer room: stealing the crystals did not deprive the ship of power.
Lt. Masters was ordered to "reamplify" the "drained" crystals. She then proceeded to do something to them in a piece of machinery we had never seen before, and after she was finished, she ordered an "experimentation chamber" prepared. At that point, one of the Lazari stole two of the crystals being processed by the machinery; later, another Lazarus sabotaged this machinery, and Masters shouted that the "energizer" had shorted, and that there was fire in the "energizing circuit". And still
the ship wasn't deprived of power!
I would like to interpret this as Masters (not a regular engineer, but a never before seen blueshirt specialist!) performing an exceptional remedial operation on four of the crystals (or crystal arrays), one that requires taking them off the actual power loop, and using an "energizer" for that remedy. Other crystals held the ship's power system together in the meantime.
I'm guessing the energizer system taps into the reactor at the base and parallels the vertical shaft and the Spock death room happens to be the top of it much like the floor machinery is the top of it.
My guess? The matter-antimatter reaction takes place down below, in a heavily armored chamber whose dilithium focus can only indirectly be accessed via the dumbwaiter system that has one terminal in that ST2-installed room. The glowing blue things are plasma conduits that take the warp energies first up, then both aft to the warp engines and up either to the impulse engines and to a power tap, or then only to a power tap that then connects to the impulse engines.
The existence of a long corridor ahead of Main Engineering, as seen in TMP, more or less precludes placing the set where Probert intended it. But placing it a bit farther aft would create no problems, except that the vertical shaft wouldn't then hit the impulse engines. Unless it diverged from vertical at some point, which is perfectly possible since we never saw the upper end.
It seems that those exact same pipes are seen serving as plasma conduits in the TNG reactor, running both parallel to the thick vertical reactor shaft and in horizontal branches that apparently head for the warp engines...