I'd like to make "L" all red - instead of red and yellow.
Not sure...may be possible, but your logo seems to be smaller. Again, patch would be essential for checking if this can be done.
And you're right. All blue letters are transparent and green was made of blue + yellow.
Using blue is a waste, solely because transparent color is blue too...
I looked up about game's mapper.
In theory, it'll be possible to expand game...reigsters allow for 2x more PRG and CHR.
So if there's need for something extra (like levels or music) it's possible but will require a lot of work.