Forgot to also mention, I have tested, and all the drives are working just fine, so putting them back into an array should work. I just need to know the process to make sure it does not format them again or corrupt my data.
Found the answer myself, Intel's software is strangely useless in this regard, but there is a workaround for anyone else who suffers the same kind of problem. I came across this post here EXTREME Overclocking Forums - View Single Post - Fixing Intel Matrix RAID 0 Which works the same way. In the chance that the link breaks I will copy them here. The steps are simple, but possibly time consuming.
"1. Reset both HDs to non-member using Intel BIOS utility - the utility warns that all data will be lost - in fact only metadata is lost and can be recreated using steps below.
2. Create a new array with identical settings as the broken array. It is critical that the HDs are in the array the same order as before. I was reconnecting the drives several times and lost track of correct order. Because of that I had to go through the steps twice (I guessed wrong the first time).
3. Get TestDisk from http://www.cgsecurity.org. I used Windows version (I installed a new Vista on a separate HD for this purpose).
4. Run TestDisk according to steps on the web site. If your HDs are connected in correct order, TestDisk should find the lost partition(s) within a few seconds. It ran for several hours, scanning my array and never found anything because I had HDs were connected in wrong order. After I changed the order and restarted from step #1 TestDisk found the missing partition immediately.
5. Have the TestDisk write the fixed partition table to the drive and reboot.
6. Now all your data on the array should be readable but the system might not boot (it didn't for me).
7. Run Vista repair from installation CD to fix the MBR.
8. Last but not least, send a donation to Mr. Grenier, the author of TestDisk."
It all worked thankfully on my raid 10 and I have recovered my 2TB worth of data, I hope this helps out someone in the future.