Exactly right. The other two films are not 70mm versions (since there are no in-theatre recordings to compare to) but are a bit more customised. Relatively minor issues, and the vast majority of both soundtracks is still the DC mixes.
The LFE channels of both ESB and RotJ come from the 2004 dvd's. Unlike Star Wars, the '04 mixes of these are for the most part exactly the same as the '97 versions--specific alterations to sound effects and dialogue appear here and there, but evidently they did not feel the need to do any other remixing aside from those instances. I don't think there were any changes to the LFE in either one, and the 448 kbps bitrate of the dvd's as opposed to 384 on the laserdiscs should offer some measure of increase in fidelity, though it's hard to say how noticeable that actually is. It is worth noting that both of them have stronger bass than Star Wars in several places. I haven't been able to find much in the way of specific references to their original LFE content and how that might differ from the SE's, so I just went with what sounds right. A lot of the time that meant no change at all, with relatively few instances of level adjustment being required.
Were you able to totally eliminate those phase cancellation issues that you mentioned? Were you able to remove the added-in LFE related to the CGI stuff added to the SE video (that is obviously not present in the GOUT video being used) and still keep it seamless (by maybe using bass from the 93 DC to make the sounds and SPL levels correct for those parts of those scenes)?
The cancellation is entirely corrected. I'm not sure exactly what caused it, but I think the upmix must have inverted the phase of some parts of the main channels, so it was partially cancelling itself out when combined with its duplication in the LFE. By inverting the LFE portion in those instances, it nows adds together the way it should, so what you hear is exactly what's in the '93 mix except more so.
Sometimes when there were CGI inserts with associated LFE content, I simply deleted them; the main channels of the original mix in those instances often didn't need bass reinforcement anyway. Other times I kept them in but at a reduced level, or substituted a modified version of a bass effect from elsewhere in the movie. Also, since the LFE of the '97 and '04 versions often differed from each other, I could pick and choose which was a better match in each case.
The most most obviously different were the Alderaan and Death Star explosions, since the strongest bass came from the added shockwaves. By splitting the Alderaan apart and crossfading it back together at different levels, I was able to give stronger bass to the beginning of the explosion while reducing the altered section; while for the Death Star I ended up just increasing the start and then fading out before the part associated with the CGI. There really wasn't much to be drawn from the '93 mix in either instance, because the main channel dynamics were given priority in that version, and its headroom would have been reduced had they included more than a small amount.