If the money difference is not a direct concern, then the 4.6 will easily out perform the 3.9. It isn't just the PEAK power, it is the extra torque trough-out the rev range, that you only get with extra displacement (or boost).
Having top hat liners fitted to either engine will be pricey. You may want to research this before proceeding.
I would also recommend a new cam and followers. RV8's are renown for wearing them, causing low power. A slightly more perkier cam would also wake any engine up too.
4.6 engines come in two flavours. The earlier ones 1994 - early 1999 use the same injection system as you RRC. From 1999 on they used a Bosch injection system and a different intake manifold. If you are getting a latter engine, then I suspect the person fitting it will swap over the intake from your current engine and use the injection system from your current one too. You'd need to do more work to retain the latter intake manifold and Bosch injection or some other standalone injection system. Which means more money.
For reference, the 4.6 block is the same as TVR used in the Chimera, only they called it a 4.5 litre.