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Hi

You have empty lines in the files that's why you have comma in the "wrong" place.
To add the count and have the output you want change the code to

perl -lane '$c{"$F[4] $F[5]"}++;...

Something like this:
$ cat file[123]
File1 xx xx xx aab rrt xx
File1 xx xx xx ccd bbt xx
File1 xx xx xx ggt iir xx
File2 xx xx xx ggt iir xx
File2 xx xx xx ccd bbt xx
File3 xx xx xx aab rrt xx...