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.
copied and paste from Rebuilding The Ford 3.0L V6 By Doug Anderson
So, given they chamber sizes are different it wouldn't be advisable to put the E6 heads on the engine that had the F6 heads. The performance would suffer.