You can get a faster turn around at some of the big builders. Money talks and bull$#!# walks
That being said, quality takes time and that makes what tyler said extremely important. Not only do the bigger builders take time because they are backed up, but because they will probably spend the better part of a day or more doing YOUR cylinders.
A full blown port job is light years ahead of a "cleanup" that some people like to call "porting".
Big distinction there. "Porting" refers to changing the shapes, angles, timing, velocity, volume, surface finish, fluid dynamics, everything inside the cylinder. A good builder has designed their own ideal cylinder and port shape, and simply use the stock piece as a starting point to create THEIR cylinder.
A cleanup does none of that, but simply improves upon what YAMAHA deemed to be best, and increase the af mixture coming in, and get the exhaust out a little quicker.
Yes you will notice a difference from a cleanup, but the PORTING (good porting) is what makes the bike a pleasure to ride and allows you to be competitive in your chosen riding style.
You should be able to give your builder your weight, riding style, planned mods, and budget and they should be able to spew back at you a recommended build without hesitation.
What it boils down to is CALL the company / person you are thinking of using and TALK to them. I don't know about you but I can smell bs a mile away. Either they know what they are talking about or they don't. They will either have a plan and vision for what will be done with your cylinders before they ever arrive at they're shop, or they are going to dick around and "try a few things" at your expense of being a guinea pig.
That being said, I can also vouch for brandon at wildcard racing. After meeting and talking to him at the mountain, not to mention seeing his stock cylinder / stock carb bike hand a few 4 mils their asses. I am extremely confident he knows what he is doing and talking about in terms of porting. He has tried many many combinations and found what works for him and what doesn't. I dont have to agree with him to know he knows quite a bit about porting and seeing his work run is even more proof.
I guess the moral of the story is there is nothing wrong with giving the little guy a chance, just make sure you feel comfortable with them by getting to know them a little, and make sure they are willing to stick with you through the build to achieved your desired results.
-Greg