Here you go neebis: http://www.sendspace.com/file/c0cb2i LFE-only FLACs for all three movies re-uploaded.
When I was first starting this project, back when it seemed like a crazy idea and I didn't know if it could actually work, I did record the LFE from my receiver's subwoofer output, since I didn't have any other way to do it that I knew of (being on a Mac it can sometimes be hard to find equivalent programs to do such things, or get Windows versions to work right). Later I discovered the program A52decX, which is what have I since used to demux the AC3 into individual mono files. Obviously this is preferable since it avoids going through unnecessary digital to analog conversion and back again, and there won't be any noise from the receiver added in. Using the LFE will certainly work added to the '93 mix without changes--the first two times I made AC3 encodes I did it that way, and only made edits later when I had more sources to work from.
I'm glad to hear you like what the LFE does for the movie. If you want to compare more of it to the straight '93 mix I'd say the Battle of Yavin is a good place to listen, and also the part where the Falcon comes out of lightspeed and follows the TIE fighter to the Death Star--the bass should be quite noticeable in those parts. For Empire, the whole Battle of Hoth is kickass, from the Imperial walkers first shaking Echo Base to the power generator exploding and everything in between. In Jedi, Jabba's sail barge exploding and the Emperor's death are especially thunderous.
I completely understand about wanting to keep things as original as possible. These versions have become my favourites, but I'd be equally happy watching the original stereo or any other good and authentic sound mix. I plan on using as many soundtracks as I can when I'm able to get some double layer encodes going. The few changes I made were basically with the aim of getting all my favourite aspects of various mixes together into one track, or as close as I could reasonably get to that.