Nah ain't gonna shout at ya
Might just take the P a bit though lol
Its a wide choice mate.
The most popular set up is the LCB exhaust manifold, with a RC40 exhaust (either a single or double silencer system), this has been used for years on Minis and proven to be one of, if not the best set up you can fit.
On a 998, you shouldn't need to go to a 2 inch exhaust system, its just way to big and will in fact make the engine perform worse!
I reckon whats happened is that the previous owner of your car had a 1275 (or bigger) and stuck the 998 in when he sold the car, keeping the exhaust and other bits on there just to keep it going.
The Minispares stage one kit is a good one. But a bit pricy, (Also as a paid up Club Member, you'll get a discount!). You can do it the cheap way and source the parts second hand though.
Don't forget, if you do decide to do it this way, stick your old exhaust and the manifold on Ebay, your should get a fair bit of your money back.
Its up to you what to do with the carb though, If it is definately a 44 then it maybe worth keeping for if you ever decide to stick a 1275 in there. If not, bung it on Ebay and you'll be surprised at what it may fetch!
As for when you fit the new inlet manifold, you don't need to connect the water pipe, its not essential. Mine is connected, but thats because the previous owner had done it and I can't be bothered to change it, it doesn't really matter!