Yeah, I do all my editing with just stereo audio and then edit the 5.1 mix separately to fit the video and stereo. If you have a clean splice at one or two given points it is pretty easy. From what you describe you want the 1983 version up until that scene and then the 97 version for a bit, and then go back to the 1983 end credits. visually the end credits can be changed after the title card portion when it switches to the crawl. Sound wise that is a harder edit. For the 97 SE the repeated a section of the end credit music so you need to find a spot before that repeat to make your audio splice that won’t be noticeable, or just fix the end credit music by removing that repeat.
That is a problem, yes. SparkySywer, how you did with the end credits? I think best would be using Harmy since when it switches to the crawl like you said and removing the repeat section in SE audio, but still you will need to switch again to Harmy audio because i think SE uses aditional music during the Special Edition credits so you can´t just remove the repeated section and continue with SE music.