I went back and did everything there is to do in Modoc all over again (starting from before I entered the town for the first time), and learned a little more about the problems I had there last time:
a) The problem I had before with Bess standing up is actually a vanilla FO2 bug, and a complex one at that. If the player uses a Doctor's Bag to heal Bess, her crippled leg is healed but the process interferes with setting the variable (mcbess.int local variable 0 bit 512) that determines whether she should stand up or not. Per's Guide to Fallout 2 mentions that the doctor skill rather than a bag must be used, but not that a strange bug is behind the whole thing; in fact it looks like whoever wrote the script at BIS intended the player to use a doctor's bag as the preferred method of fixing Bess' leg. Use_obj_on in mcbess is buggy as it currently exists, but even after rewriting and fixing that (and very prominently placing a "script overrides" command there), the Doctor's Bag itself still overrides Bess' script anyway and fouls her up. The moral of the story is, heal Bess with the skilldex doctor skill if you're going to try at all (which we knew before thanks to Per, but at least we now we know why) unless there's some way around the issue of script interference from the Doctor's Bag.
b) The problem with Balthas' weird dialogues after going to the Ghost Farm is indeed completely fixed by moving the call for a float text ("Please save my boy") to the end of his talk_p_proc (after everything else there has been processed), as Darek suggested.
c) There are bugs with both Cornelius and Farrel surrounding the watch quest--but these bugs were also present in RP 1.2 (in which I replayed Modoc as well during my search for answers--sometimes those backed up savegames come in handy). After asking around town about the watch situation and then returning the watch to Farrel immediately after retrieving it from the outhouse (in either RP 1.2 or RP 2.0), the player can still ask him about where he got the money for new tools and what's in his wall safe; both of these lines of conversation lead to the ability to demand he confess to stealing the watch or provide proof of his innocence. Since the player just gave him the watch moments earlier, obviously this is all wrong. After returning the watch to Farrel, the player can still tell Cornelius about Farrel's wall safe prompting a fight between the men. Even if one were to insist that Cornelius is senile and it's funny to instigate a fight even after the watch has been returned, looking at this in terms of the Farrel problem says to me it's a bug as well; once the quest is done it should be done. I can only guess the reason no one else reported this before even in RP 1.2 (as far as I can tell) is that nobody else ever talks to Cornelius or Farrel again after solving the quest (as there's really no reason to).
Another vanilla FO2 bug I noticed but had forgotten about: in the area around Modoc there's a random encounter called "Mantis fighting Brahmin." In all the times I've gotten this encounter, there has never been a brahmin in sight. In worldmap.txt it's in Encounter Table 22 ((6-8) DVMV_Mantis_Swarm FIGHTING (5-8) MOD_Wild_Brahmin), and everything there looks fine (correct monster pids called, etc) so I don't know what the problem is.
a) The problem I had before with Bess standing up is actually a vanilla FO2 bug, and a complex one at that. If the player uses a Doctor's Bag to heal Bess, her crippled leg is healed but the process interferes with setting the variable (mcbess.int local variable 0 bit 512) that determines whether she should stand up or not. Per's Guide to Fallout 2 mentions that the doctor skill rather than a bag must be used, but not that a strange bug is behind the whole thing; in fact it looks like whoever wrote the script at BIS intended the player to use a doctor's bag as the preferred method of fixing Bess' leg. Use_obj_on in mcbess is buggy as it currently exists, but even after rewriting and fixing that (and very prominently placing a "script overrides" command there), the Doctor's Bag itself still overrides Bess' script anyway and fouls her up. The moral of the story is, heal Bess with the skilldex doctor skill if you're going to try at all (which we knew before thanks to Per, but at least we now we know why) unless there's some way around the issue of script interference from the Doctor's Bag.
b) The problem with Balthas' weird dialogues after going to the Ghost Farm is indeed completely fixed by moving the call for a float text ("Please save my boy") to the end of his talk_p_proc (after everything else there has been processed), as Darek suggested.
c) There are bugs with both Cornelius and Farrel surrounding the watch quest--but these bugs were also present in RP 1.2 (in which I replayed Modoc as well during my search for answers--sometimes those backed up savegames come in handy). After asking around town about the watch situation and then returning the watch to Farrel immediately after retrieving it from the outhouse (in either RP 1.2 or RP 2.0), the player can still ask him about where he got the money for new tools and what's in his wall safe; both of these lines of conversation lead to the ability to demand he confess to stealing the watch or provide proof of his innocence. Since the player just gave him the watch moments earlier, obviously this is all wrong. After returning the watch to Farrel, the player can still tell Cornelius about Farrel's wall safe prompting a fight between the men. Even if one were to insist that Cornelius is senile and it's funny to instigate a fight even after the watch has been returned, looking at this in terms of the Farrel problem says to me it's a bug as well; once the quest is done it should be done. I can only guess the reason no one else reported this before even in RP 1.2 (as far as I can tell) is that nobody else ever talks to Cornelius or Farrel again after solving the quest (as there's really no reason to).
Another vanilla FO2 bug I noticed but had forgotten about: in the area around Modoc there's a random encounter called "Mantis fighting Brahmin." In all the times I've gotten this encounter, there has never been a brahmin in sight. In worldmap.txt it's in Encounter Table 22 ((6-8) DVMV_Mantis_Swarm FIGHTING (5-8) MOD_Wild_Brahmin), and everything there looks fine (correct monster pids called, etc) so I don't know what the problem is.