i was wondering y the 99 floor harness has 3 cords goin into the fuel pump and the 97 only has 2?? does this matter ?

 

3rd wire is for either the fuel tank pressure sensor or low fuel light.

 

i guess you haven't noticed that the 2 plugs going to the trunk are condensed into 1 plug on the Si harness yet. (or maybe it was the reverse of that, its been a while)
Also, some of the fuse box plugs will have to be repinned or replaced
if you have a 96-98 just get that year floor harness. its a whole lot easer than trying to reverse engineer the 99-00 harness to fit. Trust me, been here, done this.
and to answer your question, yes it matters.