Honestly, picking a combination for parts is like picking a fighter in Super Smash Bros. Some people like the karts with higher speed, some like higher acceleration. Usually, you'll have to pick between one of the two. If you want a kart with fast speed, don't expect to get to that speed so quickly (typically, your acceleration will be low). If you want a kart with quick acceleration (great for recovery), don't expect to be able to keep up with the competition unless you have good tricks up your sleeve.
Because of these, I personally like to go for the more balanced karts, where speed and acceleration is about even. Another few determining factors include weight (usually the faster karts will be heavier) and handling (unless you plan on drifting on every turn, it shouldn't be that big a problem). One combination that I really like to drive with is with either Luigi or my Mii on a kart consisting of the Birthday Girl chassis, Red Monster wheels, and the Flower Glider.
Like I said, though, results will vary from person to person. It's best if you keep experimenting and find the one combo that will work best with your driving style. There are some cool things you can do if you go to the manual in the 3DS and look on page 5. I hope this helps.