Thanks Dr. Hielscher for your reply!
The only problem I am having with the above method is that for each .ctf file (each new field of view) the data numbering is started from x=0, y=0 referring to the start of the new field of view position, so by joining it this way, mtex gives a warning of duplicity and rewrites over the previous data.
(Example each ctf file with EBSD data starts with:
X
Y
Bands
Error
Euler1
Euler2
Euler3
0.0000 0.0000 4 0 73.731 47.780 36.648
0.2500 0.0000 4 0 73.251 47.762 36.669.....
Warning: spatially duplicated data points, perceed by erasing them
The error makes sense to me, I am now trying to see if there is a way to fix this without needing to manually rewrite the ctf files.