AFAIK the 1,1 chipset actually supports 5400 series CPU's according to Intels own spec sheets (that's why this idea came up in the first place) - it's only that Apple does not support this configuration. Hence the guess that you would need firmware / SMC changes (in other words: The problem lies in Apple's part of the machine).
@OP: So far nobody has been successful in running 5400 CPU's in the 1,1 or 2,1 MacPro's, even though it has been tried. As those machines are growing outdated by the day and Apple has officially ceased support, chances are low (and falling) that someone will eventually succeed in finding out how to use 5400 CPU's in those Mac Pro's...