iTunes in a muddle since iPhone joined iPad on the account

Spot of bother ......

I've had an iPad1 for some months and just left it and iTunes to their own devices with backups and sync behaving as expected.

Last week a freebie iPhone 3GS arrived on the scene and was added to the iTunes account. No bother ........ but

I disabled autosync in order to begin selecting which apps to sync with the individual devices. Then iTunes had an indexing nightmare with some music on an external disc (in some cases it is still referenced twice for same file) and after some fiddling about with the iTunes Library.xtl and iTunes Music Library.xml a semblance of order was restored with all music transfers now being manually handled.

Now a new, and rather nerve wracking, issue. I presume because the autosync was switched off the 'apps' > 'sync apps' checkbox is unchecked. Greyed out is a correct list of apps for each device and indeed the page layouts. No problem, thought I, and checked the 'sync apps' box in order to sync. A warning popped up stating that all the apps on the device would be replaced with those on iTunes with a loss of app data. So I did not proceed. Presumably this is something to do with my messing with the two files above (the corrupt ones were removed thus forcing a re-indexing by iTunes), and presumably the app data on iTunes was lost? Or perhaps it is simply because I disabled autosync and that alone instigated a standard warning?

Looking round the net, I found the following, which deals with the problem of someone losing the content of their computer hard drive and having no iDevice backup. I do have the backups, and apart from the warning from iTunes that I was about to replace my apps/data on the device with a clean app install, I have no reason to believe anything is wrong with iTunes.

The fifth comment from 'wjosten' is the one I have found most useful:

https://discussions.apple.com/thread/2483630?start=0&tstart=0

but it does deal with complete loss. So far, I have downloaded all app purchases from the iTunes app store back into iTunes. I then intend to 'transfer purchases' from both devices back into iTunes. Presumably this will replace the 'clean' downloaded apps in iTunes with the data laden versions for each device individually?

I am not sure how much of the 'wjosten' instruction set is relevant to my current scenario. I am extremely keen not to lose my app data or layout for the two devices. Please can anyone assist? I find iTunes very unintuitive and it leaves me very uneasy.

My other option is of course to upgrade to iOS5 for the use of iCloud, but both devices run like silk on iOS4 and there are mixed reviews online from those who have upgraded.

Thanks all for any help.

Edit:

A backup of the iPhone completed okay, however, when trying to backup the iPad a message popped up stating "iTunes could not back up the iPad Name because an error occurred". No error codes, no clues. Great. It worked fine until the iPhone was added to the account!