http://www.therangerstation.com/tech_library/3_0-build.shtml
HEADS
There have been two different head castings used on the 3.0L with two different valve stem sizes, so there are actually four different heads, although
you could probably combine the early and late applications and get by with two of them most of the time.
(The chamber for the regular head (bottom) is shaped like an oval, while the one for the methanol engine (top) is more heart-shaped)
1986-7/26/99 (except Methanol applications)
The E6AE-AC/HC and F6DE-GA were built with 8.0mm valves through 7/26/99. These castings both had a 49cc, oval chamber.
7/27/99 - 2003 (except Methanol applications)
The F6DE-GC casting came with 7.0mm valves, conical springs and smaller retainers beginning in 7/27/99 and it has continued in that configuration up through '03.
1996 - 7/26/99 (with Methanol)
Ford offered a "flex-fuel" version of the 3.0L that could run on methanol beginning in '96. This head had a modified, heart-shaped 47cc chamber instead of the regular 49cc, oval chamber. This chamber was probably designed to work better with the methanol fuel that burns at a slower rate than gas, so you shouldn't substitute a regular head for this application if the customer is ever going to run the engine on methanol. These heads had 8.0mm valves along with the regular springs and retainers. They were F6DE-EB castings.
7/27/99 - 2003 (with Methanol)
Although we haven't actually seen one of the latest methanol heads, we suspect that they're still using the F6DE-EB castings. And, it seems quite likely that the later ones would come with the 7.0mm valves, conical springs and smaller retainers that were used on the later version of the regular heads.
HEAD BOLTS
Ford has used two different head bolts for the 3.0L motors. The original head bolts that were used up through '98 were 4.34? long from top to bottom. Ford increased the overall length of the bolts by about an inch to 5.50? in '99. Moving the threads deeper in the block helped reduce bore distortion which enabled the engine to make more power with lower emissions.
(Ford used longer head bolts to help reduce bore distortion beginning in 1999)
(
The threads for the longer head bolts were recessed below the deck surfacing beginning in 1999)
I'd pay strict attention to what's in this article. It seems you can use newer heads, but not the longer bolts. Perhaps someone with real expertise will comment.