Hey Richard,
Okay, first let's address the tremolo effect patch switching issue. I've noticed with the MP-2, when you create a program and you save it with certain effects on or off, this becomes the default setting for that program, so the MXC/Quad/CCP pedals allow you to modify that program on the fly.
This means if you have the tremolo set up for a clean guitar tone and you want to switch to a grind tone and still have the tremolo effect on, you'll need to set it that way in the grind tone program and save it. You can bypass the effect with the Quad switch while playing if you choose to do it that way.
Or, there is another option you might want to look into. You can also go into the RTM editing and set up the tremolo intensity to be controlled with the CCP. IF I were going to do it that way, I would set the tremolo up in the program with the intensity set to 0% as the default setting, and when you need to bring it in, just step toe down on the CCP and increase it to whatever degree you need it. (Look up the CC assignments in the manual for the intensity control number).
Like you, I never messed with the tremolo too much either since it's not one of my favorite effects. I'm not sure if the MP-2 will work this way, but I would try to set the tremolo effect up in the MP-2 to the maximum intensity I would want it to be and save it that way, then, hopefully the CC pedal will regulate it between 0% and the limit you set in the MP-2. I've never tried it, but in theory, it should work that way.
Okay, the second part of your setup with your outboard effects. One thing I was advised to do a long time ago by both Digitech and Eventide, is to put my harmonizer in the front of the effects chain so it won't be affected by the other effects. This is how I would set up my effects chain if I'm going through the loops of the MP-2:
Harmonizer/Pitch Shifter>Chorus/Flange/Phaser>Delay Effects>Reverb Effects.
I do spend some time dialing in the mix controls for each of the effects units independently from the loop mixer in the MP-2. I've have tried setting up the effects for 100% wet and mixing it in with the MP-2 loop mixer, but I've found that doesn't really sound good. So I work out the wet/dry mix in each processor, and the loop mixer in the MP-2 is set at 100% wet. I have my effects set up so I can cut each one in and out of the chain on the fly if I choose to do so.
The Powderfinger song you refer to is completely unfamiliar to me, I've never heard it, but you should be able to get what you're looking for by setting up a reverse reverb, reverse delay, or a mixture of both in your Quadraverb. I don't own any of the Alesis effects and I'm not familiar with what you have available in those, but I feel reasonably certain they should give you all of the popular effect choices that were available back in the day.
Since I did play Owner of a Lonely Heart with one of the bands I was with, I did find out that I needed several Chorus settings to get through the song. For the clean guitar parts I needed a wide, slow speed chorus to give the arpeggio notes some motion and dimension. For the clean chords, a thick chorus with some short room reverb helped fill in the sound since that band didn't have a keyboard player in it. An overdriven guitar tone with the harmonizer and a hard gated reverb, alternated with a large hall reverb with a long decay helped fill in the rest.
I'm probably forgetting a bunch of things I did with that since I'm replying to this on my first cup of coffee. But, I hope I've given you enough to get started with.