2) that Judas' Plot causes New Jerusalem to go to the bottom of the deck instead of rescuing the lost soul.
Judas' Plot actually causes the dominant of the owner of JP's choice to go to the bottom without rescuing the LS, if SoG/NJ are both played. Most often players will choose New Jerusalem, since NJ would rescue a LS regardless of whether SoG does or not, but if SoG works and NJ goes to bottom, NJ becomes a useless dominant. There are certain cases where a player may choose SoG (if it rescues the other half of the 2-liner, etc.)
Other popular "instead" cards include:
Herod's Temple--The discard from hand and deck happens instead of the discard of the NT character. So anything that would trigger from a character being discarded does not trigger if the character is saved by HT. This is especially important for Grapes of Wrath, since the discard must occur for the shuffle to occur. So if you save the EC with HT, then nothing is discarded or shuffled, and because of the new errata (instituted for this reason) no new battle occurs.
Wandering Spirit--The place on bottom of deck happens instead of the discard. This is again important with Grapes, because nothing is discarded so nothing is shuffled. This does have the consequence of making Grapes essentially an AotL vs. a lone Wandering Spirit, but this will probably a fairly rare occurrance.
I can't think of any other cases that aren't obvious (like the deck discard cards that say to put LS's in play instead--obviously nothing is discarded there) but the general rule is that instead makes it so the first ability never happens for any reason, as long as the second ability (do this instead) can be carried out. If the instead ability can't be carried out (i.e. you can't discard a card from hand or X cards from deck for Herod's Temple) then the original ability is carried out.
