I have never ground down the calipers and used stock studs, but I have ground down the calipers and used 3" studs on two different cars. One was a 03 Mach, the other was a 04 Cobra, so they both had the big brakes. Grinding the caliper and running 3" studs and some spacers was the only way to get skinnies on and keep them inside the fender. A lot of people just run 1" bolt on hubcentric spacers which allows them to keep the stock studs and not grind the calipers, but I don't like to do that, plus they stick out the fender that way and my way is track legal.
I was still able to use normal closed end lug nuts with my street wheels/tires. I was able to do this by cutting the 3" studs a little bit to where there was still plenty of thread engagement with my skinnies and I used deep lug nuts. I used 03-04 Mach 1 lug nuts in both cases because they are deeper (longer) than all the other factory ones I've used/seen. You might be able to find others that are deep enough, but this is what I found works, and what I had. They were deep enough to thread on and be tightened down enough with my street wheels/tires. As you may know, a Pro Star takes a shanked lug nut anyways. The shank allows you to use a shorter stud and still get plenty of thread engagement. (I know the pic is not a Pro Star, but I used Pro Stars on the Mach. Have pics but nothing useful.)
One thing to keep in mind when using big studs like this. I got a flat tire once in my 04. When I put my spare on and went to tighten the lugs, because of the thin steel spare wheel, my lug nuts bottomed out before the wheel was tight, so I had to crank down on them real hard and pop the end of the lug nut off. You might want to carry some regular open end acorn style lug nuts with you in case you ever have to use your spare.
Here's some pics, not the best, but I guess they help a bit.
In this pic, you can see the end of the 3" studs. (BTW, I've always used Morosos with great luck. They are cheaper than ARPs ($8 PER STUD vs $15 for a pack of 5)and from what I've seen/heard fit better. Part # 46185 for the front, 46180 for the rear) All that talk about cutting down the 3"ers a little bit that I did up there......you can see the end of it how there's no threads. I cut that part off and maybe 2-3 threads of the actual stud.
This pic you can see the grinded caliper. You can see the closed end lug; this is with those 3" studs that I trimmed down.
One more thing about thread engagement, I believe to be NHRA legal the lug has to engage 6 threads of the stud. I had to recall this the other day for someone else and have still not gotten a confirmation that it is correct, but I am pretty sure it is.
BTW - do you have GT brakes or Cobra brakes?