I think it's a safe assumption that the opening is what starts the telethon (since we see Kermit in the O of "The Muppet Show Telethon" logo being pulled up like in the opening), but I always thought the redone opening would have been a great way to either start or end the movie (though I think it's been reported that the big number outside hollywood boulevard is the ending). It could have started with the redone opening, and then at the end, right after singing the line "This is what we call...", it could have cut to black, and then we get to the opening credits and start of the plot.
And of course the redone opening could have been used at the very end, right before the credits, since the script DW read supposedly showed the Muppets getting their show back on the air at the end.