FWIW, I do my E-6 without water pumps or heaters; I just rely on my water bath to keep the heat constant enough, in conjunction with adding a bit more hot water by hand. More effort on this score might improve quality, but my method works well enough to satisfy me.
As to the rest, I've used the Kodak E-6 kit and two or three brands of 3-bath kits, and none of the 3-bath kits I've used has produced results as good as the Kodak 6-bath results. This goes double when I've attempted to re-use the 3-bath kits; quality goes way down on re-use, in my experience. Add to that concerns about how archival the results are, and the fact that the Kodak kit is less expensive on a per-roll basis, and it's just not worth it. The one advantage of the 3-bath kits, IMHO, is that they take less time to do the processing. The actual process times, if you add them up, differ by just a few minutes, but then there's extra preparation and clean-up time for the 6-bath process, and that can be a drag.
As to shelf life, when it's stored in stock form (undiluted), the Kodak kit lasts several months, at least. The kits I've bought have expiration dates stamped on their side, usually about a year in the future. (IIRC, I bought one of mine from Adorama and another from Unique Photo.) Mine have both lasted beyond their claimed expiration dates, even after being opened. If you shoot enough E-6 to be worth doing your own processing, you shouldn't have to worry about the chemicals going bad unless perhaps you buy a kit very close to or after its expiration date.