SD card textfile to char* array?

I can't see how to add an IR code to the array: char IRCodes[5][33];

You know which row the value is for, right?

Say it's the row in rowNum.

To write a character into the array for that row, use
IRCodes[something][rowNum] = someNewValue.

So, what is something? It's the nth character in the IR code you are reading from the file.

You would have a loop like this:

byte index = 0;
byte rowNum = 0;
while(file.available() > 0)
{
   char someChar = file.read();
   if(comeChar != '\n' && someChar != '\r')
   {
      IRCodes[index][rowNum] = someChar;
      index++;
      IRCodes[index][rowNum] = '\0';
   }
   else
   {
      if(index > 0)
         rowNum++;
      index = 0;
   }
}