I'm considering purchasing a Cannondale CAAD3/4 Frame and rebuilding it with parts from my Raleigh.

Do the headsets, seatposts, bottom brackets all have the same diameter threads that I can carry over all my components?

Also, will my rock shox Judy XC fork fit on a CAAD 3/4 Frame?

It should use a 27.2mm seatpost and 68mm bottom bracket. See if thats what you have. The fork will NOT fit. Cannondale frames use oversize headtubes to fit their fatty or lefty forks. You will need a reducer to fit your judy onto that frame. You will need to check if the geometry of the bike is badly affected by switching to a standard fork.

My guess is maybe to most of your parts swapping over but not without a few drawbacks.First of all,the CAAD frames use the 1.5" Headshok Suspension system,and use their own CODA headset so your headset and fork will not fit without the addition of some extra parts.A headset adapter is available from a couple of sources that will allow you to use a standard 1 1/8" headset and therefore enable you to use your Judy.There is no guarantee that your headset will work not knowing what you have.You must also be sure that you have enough steertube lenght as well.
Seatposts used on the CAAD frames are 27.2mm so you will know if your present post is the same size.
My C'Dale uses a Shimano BB but because BB's come in varying width your BB again may or may not work.
If you're going to fork out the cash for a great frame like the CAAD 4,my advice would be to buy good new parts for it or at least pick up some good used high end stuff.
Dave