Pipes will fit fine though the description of the chip is a bit vague you would be better off getting a chip specifically for your bike from JHP or similar they are not expensive i'd go for a JHP chip it worked brilliantly on my 748 with 50mm pipes and only cost £25
i'm told the 998 ECU is sealed and there for can not take a chip?? was thinking about a power commander but seen the cans and ECU on ebay and thought it would be cheaper
ECU would fuel incorrectly for your bike I think you'll find mate...
If its of interest..I can do a set of brand new 'approved' 50mm termis...a compromise in noise between full on race and legal - for £350 (dealer price £746). I am told it would be very easy to remove the baffles if you wanted full on race..
I run my 998BP engned Hybrid with a full 50mm 998S system, I have tried 3 different ECUs by them selves and none have been ideal, choices are either a Power commander or a DB tronics fueling unit, of which I have two and one is for sale.