Removing and adding new plugins

I’m still building my first multisite, well actually, I’ve started others but made a good number of mistakes and started over 3-4 times. I probably didn’t need to start over but multisite problems still intimidate me because I haven’t done a restore and have read that it’s a lot of trouble. I use backupbuddy for single site installs and love it—I can be fearless when working, knowing I have a backup plan. But with multisite, I’m not that comfortable. So I have a few questions to set realistic expectations.

1. Is it bad to try plugins and then remove them to try something else? I worry about what each plugin leaves behind. I feel like even if I remove a plugin, it can leave files behind that can or will cause problems.

I had a pretty clean install this time and was almost through with the setup and ready to develop the theme layouts but went back through the plugins to see if I could reduce the count and then started adding and removing. So now my install is not as clean as I’d like it to be. This is why I stared over several times before. Am I safe continuing with the current install or should I start over with the exact plugins and stick with them so that I don’t clutter my database? I’m not having error or warnings when testing. Occasionally it seems like a script get stuck and takes a little while to run but then everything is fine.

2. Can I use the WordPress debugging process for multisite also? http://codex.wordpress.org/Debugging_in_WordPress Or is there another process for multisite?

3. Are there any other tools/plugins that I need to check to be sure everything is running smoothly and trouble shoot before problems arise?

This is a larger task that I had anticipated. I’m hoping to have it up and running well before my annual payment is due! LOL

Thanks for your help – Jan