Many times this is dictated by the floorboard and not the header. You need about 5/8" between the top of the header collector and the floorboard to compensate for engine torquing.
The collectors are usually 3.00". So simply put, where the collector is, measure from the floorboard to the ground. Say you have 5.00". Subtract 3.00" for the collector, another 5/8" for the clearance. This should total 3-5/8". 5.00" - 3-5/8" = 1- 3/8". If you want any more ground clearance.......you guessed it, raise the floorboard, or the car.
Now if you have more than 5/8" between the floorboard and the collector it could be a few different issues.
1. Incorrect transmission installation..transmission too low in the vehicle.
2. Incorrect engine installation. Engine too low in vehicle.
3. Headers designed to hang too low (why would any company do this) OR incorrect engine and or transmission location compared to what the headers were designed for.
Keep in mind there are many different engine mount combinations, trans crossmembers, etc. that can cause issues. Most of the time if you use what the product is designed around, everything will work. It's when you start mix matching is when problems start to appear.
Aside from everything, buy as much clearance as you can.
1. Use a band clamp or four bolt flange instead of a three bolt flange at the collector. The three bolt is a triangle meaning that the point of the triangle will point to the floorboard or ground. The four bolt allows better clearance due to you being able to have a flat on top and bottom.
Better yet, the band clamp gives you excellent clearance, especially when you turn the bolts to the side. Here is an example.
http://www.afcodynapro.com/DYNATECH/706163617
Hope this all helps and the best of luck with your project!