When you want do things such as working with multiline strings that represent a board (or a matrix or whatever), the best way is to unfold the string.

Either by removing the \n, and printing the line with something like:
s/(.{$L})/$1\n/sg where $L is the wanted length; or by putting the whole board in a single string and using the \n as line delimiters.

Here I use the latter solution. You can use two regex, if your input is indeed a matrix (i.e. all lines are of the same length). First you can work the 'Y' columns, and then the 'x' line:

# replace whatever is at columns 3,4, 8 and 9 by 'Y'
s/^(...)..(...)..(...)$/$1YY$2YY$3/mg;
# set the first line to 'xx'
s/\G(x*)./$1x/gm;
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There are more than one way to do this. What is it that you specifically want to do? Replace all vertical 4's by Y's or what?

Tips: /m let ^ and $ match the beginning and the ending of a line (on a multiline string). \A and \Z match the beginnning and ending of the string. I also used the fact that . doesn't match a newline, so the second regex cannot match further than the first line.

I am not really sure it's smarter than transposition, though...