customizing a motorcycle?

If Im going to go custom I wanna go all out. Extreme extended forks and a new engine. Are chop shops willing to do whatever I want. Say I wanted a ducati 999 engine in it. Would they do it? I know all shops are different so i would need to find out from them exactly. But how does the process work? Do I just tell them what I want and they do it or are there restrictions? How about as far as finding parts or even engines? My job or theres?