Mac Pro Early 2009 freezes at password prompts

The login screen is the first moment your Mac switches to using the loaded Graphics Driver. Problems on that screen may indicate graphics Hardware problems.

Try booting to Safe Mode (hold down Shift at Startup). After running the equivalent of Disk Utility (Repair disk) the system boots up with only a very minimal set of drivers, NOT including the Graphics card drivers. The screen is drawn in simple mode, which may be somewhat slower.

Did you try a clean install? then use Setup Assistant.

Also, buy Carbon Copy Cloner and enable the advanced option to do checksum on all files copied to help insure they are correct.

While looking for a possible new boot drive, an SSD is excellent. Otherwise, zero a drive, and before you continue to use the current one, after you clone or backup the system and data, time to erase and create all new partition tables. I would do that at least on using a new OS. I would never install anything let alone a newer OS on a system that was not 200% sound and solid. Upgrade is just asking for trouble.

Setup Assistant has made it easy to keep your old system as is and bring what you need along but leave the old one intact - and hopefully as your safety net in case the new system has its own issues.

The spinning gear is presented to avoid overwhelming you with the Terminal commands as they go by. But those commands, if you could see them, would tell you what is going on while you are waiting so long. They can be inspected out of the system Logs with console.app, or you can see them "live" by invoking Verbose mode (hold down command-V as you boot up)

When the system starts up in Verbose mode, so many lines scroll by that they roll off the top of the screen. If you are not seeing something like that, you have not managed to invoke Verbose Mode.

Your complaint was that startup seemed to stall. The messages stopped at ... something. The thing they stopped at is likely the source of the problem. Please post the last 10 messages, or from BOOT TIME to when the message stop (fetched using Console.app). You may have found the culprit.

If you are finding the use of this computer overwhelming, then it is probably time to visit your Apple store. Your appointment at the genius bar at an Apple Store for an evaluation is free, in warranty or out, and if hardware is needed, repairs are mostly done at flat rate (no surprises). But there is no obligation to have them do anything for a fee.

Windows talks to the hardware different, has more drivers to support a wider range of products

You have these two items:

NVIDIA Quadro K5000M 4096 MB

3TB ST3000DM001-CH166 OS X boot drive.

I would want to try a different GPU if possible - even a PC card and just know you won't see "early boot" or EFI boot manager (via Option key) -

I definitely prefer to use and see a 250-500GB SSD system drive (esp. Windows)

Then clone Windows to another drive (Paragon HDM 14, or Carbon Copy Cloner 4.0 for OS X) as backups and then pull either the new clone or the old system - and always have Windows and OS X on their own separate disk drive. And data on its own drive - NTFS for Mac from Paragon is perfect for using NTFS and sharing iwth both, or there is Paragon HFS+ but which I don't care for as much.

You posted output from etrecheck? www.etresoft.com

Then install one of the better sensor monitoring apps like iStatPro or Hardware Monitor (Temperature Monitor too which is free but lacks some of the reporting and monitoring features). And, "less is more" and the less junk or err "extras" to modify a system the better.