http://www.sw-em.com/SU_vs_disp.jpgI love this chart. You can put the twin carbs but they're not really necessary for a fast road 998. They are complicated to tune and have twice as many parts to refurbish or upgrade. They are hs2 not h22.
Su carbs suffer badly from worn spindles, to stand any chance of tuning them properly get them checked out and refurbished if neccesary.
Absolutely no idea what the gear is about, more info needed.
The 12g295 is not an instant upgrade, you have to carefully measure the compression ratio of the original setup to at least stand a chance of achieving the same compression ratio. If you don't it could be a step backwards in terms of power.
What comes in must go out, have you put thought into exhausts? Is the current engine in good condition? Can you even use it or will more power put it under too much stress?
Don't be offended but I am sensing you're new to building engines and minis in general? They are fun little cars and a lot of people out there have the information you need. They just cost coin, so find a good specialist and pay for some of their time.
Listen to the doc, you have a small bore, not a 1275. If you bore out a 998 too much best case you get horrendous oil consumption, worst case you get a door stop.