Hey Dude,
As I said, the Plexi is workable. If you are super picky and have a need for every tone to be spot on perfect, you may need to keep your clean module to ensure you can maintain that level of maturity.
Personally, I think it is a matter of taste and personal style. My style is a bit looser, and if I had to record a clean tone with my current set I would probably use my tweed module. If I was playing a song that required some cleaning up and I had the plexi in the rack instead of the Tweed, I would just roll back the gain and play.
I have never used the Deluxe or the Top Boost as of yet so I cannot speak to their tone. I personally did not care for the clean module. It was too Jazzy sounding no texture. I like texture in my music. I have a top boost coming, and am excited to hear it.
If it is a choice between the Plexi or Clean, which is what you asked, I choose the Plexi and live with it which you can.
If you have other choices, what about the JTM module? I just sold mine, but it cleaned up way better than the Plexi or the Tweed I have. I only sold because it was soo close to a cross between the Plexi and the tweed to my ears. Not exact of course, but close enough for me. I am also just getting to know the 1086 I just got, and it may actually replace the Plexi since it can bascally match the Plexi, but has a more diverse range of tones. May be a better option than the Plexi if you can only afford one.