Finally getting back to you about the scripting... Do you think you could make scripts for some of the NPCs in Saffron City? I'll need scripts for person event nos. 9, 10, 11, 14, and 15, so you can check their scripts and see what their original dialogue was like. They'll actually need two sets of dialogue: one for before Team Rocket takes over Silph, and one for after Red defeats Team Rocket. I've got the flags rigged up so that the NPCs will disappear while Team Rocket's in control and come back afterwards, so you don't need to worry about hidesprites. The flag I'm using to signal Team Rocket's defeat is 666. (It was easy to remember...) Pre-takeover, Saffron citizens might sorta be able to tell that the Player they're talking to might be with Team Rocket, but they won't know anything about the imminent takeover. Post-takeover and liberation by Red, they'll know full well that the Player is a Rocket.
Don't worry about offsets, I can assign offsets and compile them into the game myself. Just let me know which script goes with which person event no. Thanks.