if you remove the wedges, then yes you'll need to fill the holes, some people use rivets, but unless they are solid reaction type rivets then you'll be safer fitting some small nut and bolt combination(loctite a must on these).
51mm throttle body works well on GT manifold set-up, but you'll see little benifit from it until your into the higher RPM's, once at this stage then you can look at smaller pully's, headflowing, cam's, injectors, FMIC etc
Don't forget your brakes, suspension and gearbox too!!