Ooo, really excited to follow this.
For your key question, they do spawn in acts as soon as the Chao are all collected. No need to replay acts. So of course map Chao should be grabbed before entering the 3rd Act you do of a Zone.
I'm assuming from that question you are not aware of the SDA run by mike89
here. (or on his YouTube.) Even if you don't watch the video, I'd check his notes as I do recall it has some info on how the keys seem to spawn.
As for your issues with the VBA and the reset, some versions of the emulator just don't support resets in the movie recording. When I have a sec I'll try and find you one that did. I forget if it was a standard feature in the later builds or not.
Edit; Looking at my files back at home, I've always had the 1.7.2. re recording v19.2 version for messing around with his run. But after a quick test knowing that, the first download under 'old downloads' at the emu resources on here,
http://tasvideos.org/EmulatorResources/VBA.html , the 1.7.2 v19.4.zip, got past R99 boss to the character select and back to Sunset hill. I'm sure there is a better option, but till someone more knowledgeable gets back to you should be good to go with with that.