I had ghost images as well as a standby (offline) drive mirror to slam in, and I still did the staged upgrade. You're almost certain to run into one or more problems and doing each component one at a time helps to isolate the problem. I'd rather do it a little slower, fix problems as they arise, then push too far, too fast, too soon and have to revert back to an old backup. but that's just me.
RIM advised me to do a similar upgrade as Jadey.
1. Upgrade O/S
2. Upgrade Domino
3. Upgrade BES
RIM likes to see Domino upgraded before BES, even if you have to temporarily run with an older/unsupported combination (new domino / old bes).
I get a feeling RIM gets uneasy when dealing with old builds of Domino. It may be a comfort factor on their part. and given that we Domino admins tend to be better/more knowledgeable on the Domino-side than the BES-side, it might do us good to head RIM's request on this one.
From me, #1 was a knife edge cut over from NT4sp6a/R5.0.7/BES2.2.6a to new hardware with the same build of Domino and BES - 2003sp2/R5.0.7/BES2.2.6a. Ran that for a few days. #2 The did an inplace upgrade of Domino to 6.5.6FP1 (was the latest at the time). Ran that for a few days. #3 Then I did an inplace upgrade to BES 4.1.4 (the latest at the time). Will probably upgrade Domino to 7.0.2FP2 in the near future, if need be.
If you have TSupport, you might call into RIM and get a different answer or suggestions from them. I don't know.
As for the upgrade to Domino R7. Except for my BES server, all of my domino servers (6 of them) were on 4.6.5 or 4.6.7(intl). IBM told me to got from 4 to 7 required a two step process, requiring me to got from 4->6.5->7.0. I don't recall if 5.0.x had that limitation (needing a 6.5.x interim upgrade first) or not. But I'd verify that with IBM Lotus.
Of course with the upgrades you'll want to make sure the Domino server service is off. ditto with the BES services and the Domino BES tasks. Then bring them up manually and check things. There's also some DB maintenace tasks/housekeeping you should do prior (plus clear out the pending Administration requests (admin4.nsf), clear out the router mail boxes (mail*.nsf), etc). It's also a good idea to audit the items in the notes.ini, since some of the settings are different or depricated in Domino R6 and R7 now.
One thing I noticed on my 5.0.7 to 6.5.6 upgrade was that Domino added
a DSTLAW= setting in Notes.ini, a setting that was purported to be depricated in that version. That was odd.