I had this same thing happen on a phone I just exchanged, it would seem to take 5 minutes to reboot, and during the process it would almost look like it booted twice. It would boot, I'd get the thunder and animation, then the screen would go blank for a bit, the clouds would reappear without the lightning and it would sit there for awhile. The problem for was that in this process it would occasionally erase the memory card, to the point, where I had to pull it and each time and format in PC, it would not format in the phone.
I tried factory reset, but the problem continued, so I think there was some sort of hardware fault in the memory card reader that was causing the phone to hang during boot. Since exchanging the phone I haven't had any spontaneous reboots, but restarts now only take about 1.5 minutes when I exchange the battery. The contents of the SD card are basically the same as I restored all my apps, music, books, etc.
My point being is that if it is taking 5 minutes, you may have some sort of hardware problem-- have you had any issues with the memory card? Just grasping, but my experience with the replacement phone so far is SO much better than the original, battery life is better, no erased memory cards, no spontaneous reboots..I'm back to loving the phone instead of considering throwing it against a wall