As far as I know anything over the 3.5 had liners (think there was another without)
Your 3.9 has liners. It can be stroked to alot if you are brave
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As I said earlier the 3.9 is the same as the 4.0 they changed it when they changed the engine management.
The 4.6 crank ++++bits will fit in the 3.9 and suddenly you have a 4.6
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But with all mods from standard brings more expense.
When I got the "new" 4.6 I was offered 5.2 but of course then you delve into needing new fuel maps for the ECU.
Tophat what you have and it will be a very reliable V8 with standard bits readily available.
J