My wife and I have same email account. can we both use iCloud?

You didn't mention this, but I assume you must have an iPhone too. Assuming that's the case, you can set up the same iCloud account on both phones if you wish, and sync your contacts, calendars, etc., to the same account. However, when you do this both the data you sync will be merged and you you will both end up with each others contacts, calendar events, etc. on you phones. If you don't want this, then you need to set up separate iCloud accounts using different Apple IDs. If you elect to have separate accounts, you will have separate iCloud email accounts as well, but you don't have to use them. You can still set up your joint email account on both phones in addition to your iCloud email account, and continue to share your email as you do now.

I unchecked the email addresses that were on both the touch and the phone. I then got notifications that it was changed on the ipad as well. Put everything back the way it was. If I create my own Apple ID and icloud, can I sync the common calendar, email, itunes, etc? What I need is to be individual with facetime and imessage stuff and common with all the rest of the icloud service. The whole point was to stay connected to home as I am forced to use a BlackBerry for at least another year at work and I dont want two phones.

To separate your iMessage and FaceTime and leave everything else the same use a separate ID for these two services. Decide who will be changing to the new ID, then on their devices go to Settings>Messages>Send & Receive, tap the ID, sign out, then sign back in with a separate ID. Then do the same in Settings>FaceTime. You don't need to change anything else; you can continue to share the same iCloud and iTunes account.