Restore from iTunes breaks wifi, iOS 6 to iOS 8

I recently switched from a 3gs to an unlocked apple factory refurb 4s. I used restore from computer backup on iTunes to transfer data and set up new phone.
Phone functioned fine for about 2 weeks, and at that point, wifi failed. Traded it in on warranty for another one, restored from iTunes again, and both wifi and bluetooth failed in less than 24 hours.
Tech at Apple Store said that restoring from computer on iTunes can put old, vestigial code on new phone, which can break the phone. He said I should set it up as new phone, and use iCloud to transfer data. He helped me set it up and do that, and while the process is not complete, it appears to me that there is no way to transfer some data, particularly on iMessage, onto the new phone. There is data on there that I need to retain access to. Is there any way to transfer that data to the new phone with out restoring from backup on computer? Alternately, is there anyway to set this new phone up by restoring from backup on computer without breaking it?

I am in the same situation. I tried to update my ipad with IOS 8. I have successfully downloaded the software and when I clicked install the ipad went into recovery mode. I assumed that its part of the upgrade process. It asked me to connect to iTunes which I did. This never happened in any of the previous upgrade. How much ever I try the ipad never got out of the recovery mode. The only way was to restore the ipad. I assumed I would get an option to restore from the last backup which I did last night so I was confident that I am not losing any data. Surprisingly it never gave me an option from where it could restore and went all the way to restore to factory settings. And alas I see the ipad is restored to IOS 8.0 but with factory settings as brand new one. And now I don't see any of the previous backup's even existing. It has erased all the previous backups.
Can you f...ing believe it. Apple can get so dumb ...no one could even imagine. It think it all died with Jobs.

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