Hey everyone;
There has been a lot of talk on the forums about shorty headers for our sixers and there have been lots of idea's about them. I am here to show you why you need to keep your 94-98 Headers and swap those old 99-04 Logs out for a set of 94-98 headers!
First off I will show your the size differences of the two, starting with the 94-98 Headers followed by Pro's and Con's.

---------- 1994 - 1998 stock Headers ----------
Collector Size 2 1/4"
PrimaryOpening1 13/16"
PrimarySize 1 9/16" OD
Flange Thickness 5/16"

---------- 1999 - 2004 stock Manifold ---------
CollectorSize 2"
Primary opening1 9/16"
Primary Size 1 3/8" OD
Flange Thickness 5/16"
Just comparing these you can see how much larger the 94-98 Header really is. Here is a short list of Pro's and Con's.
94-98 Pro's and Con's
Pro: Superb flow
Pro: Large 2 1/4" Collector
Pro: 3-1 Header
Pro: Not prone to cracking
----------------------
Con: D-Side has factory kink in rear cylinder
Con: Firecone can have excess slag that needs to be removed
Con: O2 sensor in collector. Hard to get to.
Con: Uneven style
99-04 Pro's and Con's
Pro: O2 not on collector
Pro: No slag to restrict flow
----------------------
Con: Prone to Cracking
Con: Log Style
Con: Restrictive
Con: Small 2" collector
A note that I feel is very important is that I measured the exhaust ports on the 94-98 and 99-04 Heads as well. Here is what I discovered.
The 99+ splitport has an awesome intake side to the head allowing large amounts of air into the head, unfortunately Ford made the exhaust port smaller than previous years 94-98 Single ports creating a large bottle neck. Don't worry though, this can easily be ported with a flap wheel sander even while it is in the car!
Exhaust port shape doesn't mater a difference in the headers or flange.

94-98 Single Port Heads (D-Shape Exhaust Ports)
Side to Side: 1 1/2"
Top to Bottom: 1 1/2"
Corner to Corner:1 11/16"
----------------------------

99-04 Split Port Heads (O-Shape Exhaust Ports)
Side to Side: 1 3/16"
Top to Bottom:1 3/16"
Corner to Corner: 1 3/16"
I hope this has helped everyone out. Tell me what you guys thought.
Note: When using 94-98 Headers on a 99-04 you need to have a shop enlarge the inlet by 1/4" and bring your 94-98 Headers down for fitment. A muffler shop charged me $5 per expansion on my trucks exhaust. Its cheap and easy
-Eric-