I have 2 disks with 3 partitions in a RAID 1 mirror (md0,md1,md2).
Now it looks like one of the disks has failed and two mirrors are broken.

Now it would be quite an easy fix had the failed partitions been on the same drive but that isnt the case, I have bought two new drives but unsure how to replace the whole mirror (system only has two SATA ports).

Any ideas on how to get this fixed?

Contents of /proc/mdstat:
md1 : active raid1 sdb1[1] sda1[0]
40064 blocks [2/2] [UU]

md2 : active raid1 sda2[0]
2626560 blocks [2/1] [U_]

md0 : active raid1 sdb5[1]
309660800 blocks [2/1] [_U]

Not sure I follow you. RAID 1 protects against a single drive failure. If one HDD has failed, then all mirrored partitions are effectively broken and you remove the failed drive and replace it and then rebuild the array.

If you have had both drives fail RAID 1 cannot protect against this. The best you can do is retrieve as much data as you can from the failed drives and replace the entire array.

If you are having problems with particular partition(s) only, check the state of the drive for errors. To retrieve data if you have multiple drive failures/corruptions, remount the drives as individual drives and copy off the data. You can rebuild the filesystem from as much as you can retrieve from eh two drives.

Can't you take a[nother] backup of the partitions, then replace the drives, rebuild the RAID scheme and put back the backup?
That said, if it's just corrupt data can't you just rebuild the RAIDs as is then swap one drive, rebuild, then swap the other?