What ho chaps. Nice to see you back up and running. I was getting worried.
Anyways, I've had a full playthrough of the game as a light side guy. If you've yet to see some parts of the game, spoiler alert!
Bugs I've come across:
Lightsaber Graphical Discrepancies: This would cause the game to break, but I fixed it by disabling Vertex Buffer Objects - just so anyone else getting that trouble knows what to do.
Ebon Hawk: As well as the fact that G0-T0 does not acknowledge that I am the saviour of Telos' fuel supply (as the OP posted), after the events succeeding your second trip to Onderon, I met Atton outside the Ebon Hawk, for he had been the one I'd sent to the tomb of Freedon Nadd as the leader of the group. Even though he'd chosen the light side option at the final battle, he came back with a full dark side rating. Likewise, other members of the Ebon Hawk crew who had previously been light side-oriented now had dark side ratings, as well as the facial changes.
This happened to Bao-Dur, Visas, (Atton was fine once inside the Hawk, oddly enough) and Mira, and did not rectify itself throughout the rest of the game. Instead, I had to manually change the light side points via the cheat hub, and when I tried that on Atton it actually reversed his and the Exile's alignments. Very confused, and wondering what the problem is here.
Dantooine: The vanilla crashes that occur after the Battle of Khoonda. Since this isn't the Mod's doing, I'm using this as a warning - have a save ready during the final moments of the outer battle of Khoonda and you should be able to plough through the game-breaking area after defeating Azkul (light side assumption here).
Nar Shaddaa: When picking people for the fight through the Zhugs (at the platform with the Ebon Hawk), for the third person the black borders on the top and bottom, signifying a cutscene (yeah, I don't know the technical term, hope you catch my drift), disappear, leaving only the options. It's quite jarring and puts off immersion, and practically screams, "You have transitioned into a restored part."
The Endgame: The final moments in the Enclave worked brilliantly, and I loved the added dialogue there. The part with Atris seemed fine as well, though I wasn't sure if the Handmaidens were supposed to disappear like they did, once called into Atris's chamber (I was playing canonically as the female Exile, which I hadn't done before, so there was no Brianna to fight the Handmaidens; instead the Exile traversed a disturbingly deserted Polar Academy - I also found no corpses, is this intentional?) .
I loved the HK-50 Factory, and the events therein. However, the BIK movie for Darth Nihilus's invasion of Telos occurs both before the factory, then after the factory, which is pretty confusing. I also managed to f**k up the ending by not turning one of the two HK groups to my side. I still don't know how to do this, and would be grateful if someone told me.
The battle for Telos went well, and the Ravager parts did too. I liked the new dialogue between Visas and Mandalore - explained a lot.
Malachor V: Here we are. That place. Is it just me who gets filled with a sense of dread when I even hear the name of Malachor V? Anyways, one of the BIK movies didn't play for this part of the game - the one where the Ebon Hawk comes out of hyperspace and you finally get to witness Malachor V. Instead, it just had the part where the Ebon Hawk is brought down by the storms. Before that part, Kreia kills all the Sith Assassins and confronts Darth Sion. Either I accidentally managed to skip the BIK depicting the exit from hyperspace, or it just isn't playing.
When HK-47 interrupts the Remote and G0-T0, and G0-T0 simply takes control of HK-47, I discovered the fault was mine for not "recruiting", as it were, either the HK-50s or the HK-51s. I don't know how to do this, and would definitely like to, because I believe it contributed to my game's ending (it played the Dark Side BIK rather than the Light Side, Mass Shadow Generator's activation BIK - this confused me considerably and ruined the end for me because of my own screw-up).
And finally, the Trayus Academy. I enjoyed the fact your companions make an appearance (in the vanilla version of the game I thought everyone had died, especially when the Hawk fell to what seemed an ignominious demise - I see that the BIK for that doesn't play, but I also assumed that that was done on purpose), though I didn't understand what happened when I was told I had two choices on a path to take, and one choice involves saving them. I chose the prison cells, and couldn't find my companions, though I did find a room that was clearly meant to house them. Were the companions supposed to be restored to this room?
The final battle with Darth Traya went well, and I enjoyed the part where you leave with Atton, him making quips (it really went far to making it feel like an ending), but again, as I said, the Dark Side BIK played for the ending, as I'd done something wrong (well, for the light side role I was playing) at the HK factory.
Hope that this bug report helped out, as I mentioned quite a bit. Of course, these were just the problems I encountered, so there might be others. Nothing game-breaking except the vanilla bugs, just immersion-breaking. I'd appreciate a response on my HK Factory screw-up, and on any of the other bugs mentioned in general from anyone with knowledge on the matter (and of course, preferably the valiant modders).
Cheers. And of course, I find the Mod is brilliant - completely worth the wait!
Edit: Also, I have Version 1.6 plus the Nar Shaddaa fix. The other mods I have were specifically stated to be compatible with TSLRCM.
Those mods were: Prologue - Peragus - Harbinger Correction Mod (1.1)
Sion's Arrival to Peragus Fix
and Coruscant - Jedi Temple.