My timeline is in my signature. Unfortunately, CIC is very inconsistent, and there's no real way of knowing just how long your app will take. The best you can do is do a lot of reading, take care with your application, include everything that's needed, and hope for the best.
If you submit your application inland, the sponsored person is supposed to remain in Canada for the duration of the process. Your wife can always leave, but if she is denied re-entry, then the application is void, your money and time has been wasted, and you have to start over (AND you have to report the denial of entry as you put together a new application). Some have traveled and reentered Canada during the process with no difficulty. However, for me, I thought the risk too great. If I got that one Immigration officer at the border who was in a pissy mood, and I got denied (despite being an American, and visa-exempt - it happens, my husband personally knows one man whose American wife was denied entry at the border), I would be CRUSHED if we had to start over again.
I don't know much about the OWP, as I didn't not submit one, but I do know you cannot apply online before AIP is received. You must submit a paper application for OWP with your PR application, and yes, it is granted when AIP (first stage approval) is received. You get the paper permit in the mail a little while after getting the AIP email.
