http://www.enginebuildermag.com/Article/2179/rebuilding_the_ford_30l_v6.aspx
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.
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.
HEAD GASKETS
The head gaskets can cause some confusion if you're not aware of the differences between the FWD and RWD gaskets.
RWD
There are two different head gaskets for the RWD engines. There's one for the left and one for the right, and they both have to be installed with the "UP" that's imprinted on them facing the head or the engine will leak coolant or overheat or both. When the gaskets are installed correctly, they both have a slot in the back that allows the coolant to thermosiphon up from the block and into the heads so it can flow forward through the heads and cool them before going into the radiator.
FWD
There's only one FWD head gasket, so it fits on both the right and left sides, but it still must be installed with "UP" facing toward both heads or it will leak, too. The FWD gaskets have two smaller coolant slots on both ends so they can't be used on the RWD engines because the coolant won't flow through the heads correctly.