In order....
Normally documents have a section that addresses "Multiple Employer Provisions". Do you mean the Plan has "multiple employer plan" in the name? If so, just change the name. If something else, I need more details.
A Multiple Employer Plan (MEP) will have a "primary plan sponsor". The other firms are "adopting employers". It sounds like your client is the "primary". It is analogous to sponsoring a prototype. The analogy does breakdown qucikly, but it might help you visualize this concept.
Have "adopters" terminate their participation. Keep in mind that the plan is simply a program that is sponsored by the primary which is adopted for use by the adopters. Ultimately, you could have the primary terminate sponsorship, but that requires steps that I am not sure you need at this point.
333? Sounds like whoever had this before you was trying to apply "logic" like plan number 501 for 125. Anyway, on the next 5500 you do, take action to correct plan number. See 5500 instructions for details. It's not hard.
Your conclusions about the Adoption Agreement confirms that this firm is the primary.
No comment comes to mind.
It already is a "regular 401(k) plan". You just need to clean a few things up. Almost all can be done with the EGTRRA Restatement. Of course, you may have some historical operational defects, but without details, I can't speak toward that. Assuming that there is not serious "botch up" with the past administration, you should be able to fix this without too much problem. Of course, Murphy's Law says......
Hope that helps "Pat".