I'm new to this but I'd be doing something like

open file1 for input
open file2 for output using >> so it appends
.marker1.
read a single line as variables $1, $2, ...
use switch/case to select the field(s) you want to fix or alter
change it(them) for that line of input (with case selecting fields you
+ want to alter in order)
print to (output) file2 the variables $1,$2...
check if endof input file
if not goto the next line of the input file
loop to .marker1.
if eof input file
add a print "\n"; to the output file (you usually need it)
and close both input file and output file
[download]

simple I think, but i'm a newbie