W/o knowng the nature of your business, the length of the engagement, and the specific relationship between the partner Firms it's really difficult to make any specific recommendations for your questions. Personally, I'd err on the side of keeping everything at "arm's length". As a partner in such a venture, I'd want to be sure that my other business concerns weren't getting mixed up in this project, and I'd want to see the same for the other partner(s) involved.
Depending on the need for "realtime" collaboration, I'd consider keeping all the data in some "cloud" solution. I'd either contract with a hosting provider for data file storage, revision control, etc, or put up servers specifically for that purpose (ones that aren't used for my "regular" business). Something simple like a wiki engine might be all you need, or you could look at something that integrates a revision control system (Subversion, etc). I'd want to work out a protocol with the partners about who performs IT administration duties for this hosting solution (performing backups, controlling access, monitoring availability, etc).
re: sharing an SMTP address space: If you're concerned about "leaking" out the email addresses of the partner companeis (instead of the shared "unified" domain name) then you'll probably want to keep the email out of the affected users' "regular" email at each company. It's a pain for the users, but having to use a different email client / webmail / etc, versus something like "Remember to change your From: address when replying to Customer xxx..." is likely going to be problematic. If your MTA is smart enough to support selective mangling of the "From:" address depending on the recipients specified in a message you might get away w/o this.
I'd consider contracting email delivery for the shared domain name out to a third-party MTA. Have that third-party deliver incoming messages to the appropriate SMTP addresses at each partner company (in their own SMTP address spaces) if you want to intermingle the shared domain email with each partner company's regular email, or have them host web-based email for the partner company addresses (to keep it separate from each partner's "regular" email).
Like I said, it's hard to make many specific recommendations. Hopefully there are some ideas there that are helpful to you.