It is perfectly ok to run a Mac Pro or any Mac with Windows only. The only thing that you can potentially miss is a firmware update. But EFI updates are so seldom that you should not really care. And once your machine runs with Windows it will not really make a difference anyway. You can still catch up with an update when you come back and re-install OS X.
With Windows only you have a wide choice of drive setup. You can use the Apple method with the OS X install DVD and use the GUID partition table. The other option is to install Windows directly from the Windows install disk which will give you an MBR partition table. Both methods are possible and will not have an impact as long as you use Windows only. The GUID table is better if you later want to make changes to the drive like adding an OS X partition. In any case I would take my OS X install disk along with my Windows install disk on a trip.
Regarding SATA performance I have never seen a difference between ports. Some people swear they have but it shouldn't be a problem for a Windows only machine. By any means use #1 slot for the system and apps and it should be ok.
If you partition one drive with dedicated partitions for the system and for data that can push your system down on the slow part of a drive. This may have caused the rumors of slow Windows drives in the first place. In such a case it is best to use different drives for Windows booting and for data. It is actually very sensible to have different system and data drives. You have a pretty big chance your system gets corrupted and needs to be rebuild due to viruses or user mistakes. The copy protection in Windows makes the system fail very quickly if you make changes that may seem entirely logical to an OS X user. So different drives will protect your valuable data and make system rebuild faster.
The realistic issue for SATA performance in Windows is the use of the driver. For full performance the Intel AHCI driver is required which will only run with a patch to the MBR of the Windows boot drive. Reference to the Howto:
https://forums.macrumors.com/threads/760482/
Something to think about in that situation is backup. If you fit an additional drive you can use Windows internal backup mechanism to make internal backups and you would not loose too much work by a disk failure. The system can be set up for automatic backup of additional data every day. If you are concerned with the physical safety of the location of the machine you can also use an external drive for backup and store it in another place. My personal preference in your shoes would be a system and apps drive in bay #1, a data drive in bay #2 and a backup drive in bay #3. All of them set to NTFS.
Another option would be fitting a new OS X drive or a clone of the OS X drive which you want to leave at home. You can then use Winclone to make copies of your Windows drive on the OS X drive. By this method you will not be able to make differential backups and it would take much longer to secure your work.