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;
}
}