Installing new internal hard drive. How do I safely clone my existing BOOTCAMP partition?

I have a 13 inch Aluminum Late 2008 MacBook. Processor 2 GHz Intel Core 2 Duo, Memory 4 GB 1067 MHz DDR3, Software Mac OS X Lion 10.7.4 (11E53). Currently I have a 160 GB SATA disk as my hard drive a d 4 GB of memory. (Is it time to upgrade or what?) I recently bought a Western Digital 1 TB internal hard drive to replace my exisiting internal hard drive. I spent a lot of time last night trying to first- connect this new hard drive to my computer so that I can then clone the existing hard drive and then hoping that I would get that done so I could install the new hard drive. No such luck.

My current hard drive is partitioned as follows:

Name: Macintosh HD

Format: Mac OS Extended (journaled)

Size: 132.5 GB

Name: BOOTCAMP

Format: Windows NT File System (NTFS)

Size: 26.69 GB

When I was partitioning the new drive I did so as follows:

Name: Macintosh HD

Format: Mac OS Extended (Journaled)

Size: 973.51 GB

Name: BOOTCAMP

Format: MS-DOS (FAT) --- This was the only option that I was given that I thought would work. I did not have the option of "Windows NT File System (NTFS) to choose from. Question # 1: is that going to be a problem? I only run 1 program on Windows and that is the only reason I have BOOTCAMP on there at all. However, I do HAVE to have that program. Like I said it didn't give me the option to choose Windows so I didn't know where to go with this. Any help with that would be awesome.

Size: 26.34 GB (I just used the same size that was current, or close to it.)

I connected the Western Digital 1 TB through an external device, partitioned it as stated above, and then used Carbon Copy Cloner to clone the drives. The first one went through fine. (It took 2 hours and I went to bed before it finished.) This morning I woke to see that it had gone through well. I then started the process with the BOOTCAMP drives. However, before I started it gave me errors stating that I wouldn't be able to run Windows off of the Cloned BOOTCAMP drive. Question #2: Is it because of the Format type I chose when partitioning? Or something else? I am unsure where to go from here. I would really appreciate any help that is out there. I would love to get this new drive installed ASAP. Thank you so much in advance!