The MAIN reason to do the J-mod is that it is actually better for your transmission. Larger holes = more rapidly filled accumulators = faster shifts = cooler fluid and transmission components.
As far as the shift firmness is confirmed, the J-mod is still better than a programmer. Been there, done that. It firmed the shifts up more than a programmer ever did on my car, and actually made the part throttle shifts better as well, unlike a programmer. There is a reason why Jerry Wroblewski, the engineer of the 4R70W, recommends the J-mod: because it is better.
The articles that nyuk98gt posted are very helpful. Go read them and get familiar with all the terms and components. When it comes time to do the install, here is write-up that I followed:
http://www.crownvic.net/tech/4R70Wnotes.pdf And here is the thread I created after I got done with it:
http://www.stangnet.com/mustang-forums/threads/jmod-done-the-smile-on-my-face-much-bigger.822975/
If you are nervous about tearing into your transmission, don't be. I had never touched my transmission before I did the J-mod. It was very easy and straightforward, and it only took a few hours total on my first time. If you want to get picky about the time, you can go out RIGHT NOW and buy the tranny fluid, drill bits, and any tools you may need, and DO the J-mod before your programmer comes in the mail.

And it's $300+ cheaper as well.
Oh, and also. Late '01-'04 cars don't need the J-mod nearly as bad as pre '01 cars. The newer cars already came with slightly modified valvebody separator plates and accumulators. So while there still will be a difference, it won't be nearly as pronounced as on a car like mine.