considering you are going from one pump to two pumps I would say you need a re-tune. Or at least have it checked/tweaked. You also might need an 03/04 cobra FPDM or dual FPDMs but i'm not sure on that.
So it's just straight forward plug an play and just cut an cap the extra line that comes off the filer neck on the 99 cobras? But I still need to get it tuned?
on my 99 cobra i needed my tune to be adjusted . I had a Amazon tuning solutions mail order tune and the owner just made a couple of tweaks to my current tune .. Before that i could drive the car but it would cut out/buck as rpms increased . So yeah you will need a tune ..