After searching on these forums and finding the cheat code to set my canister usage in Geneforge 2, I compiled the following additional codes for other flags that seem to affect the ending (mainly to see the ending text if I didn't find Shanti). Bring up the cheat console with Shift-D and enter "sdf x y z" without quotes, where x and y are flag indices and z is the value as respectively described under each description below. I.e., "sdf 100 7 0" to set canister usage to zero.
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Warning 1: Make a back-up of your saved game. I didn't test everything and immediately left the valley after cheating, without continuing the game with the cheats.
Warning 2: Spoilers below.
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Edit: The above are all the flags that I've found that seem to affect the ending text (unless otherwise noted). For others, it's easy enough to search for get_flag or set_flag or sdf within the script files anyway.