The 4.6 does as you say have a longer stroke than the 3.9.
Are the blocks the same?
Depends on the age of the 3.9, IIRC 3.9 blocks from '95 onwards were cross bolted, earlier ones weren't, but yes you can use a manual gearbox with either (my 4.6 110 is a manual at the moment).
As for tuning any Rover V8, forum member Fridge Freezer has been known to say it's like "polishing a turd", might sound harsh but he is correct, the RV8 is a very old design, yes you can improve it but it will cost you lots for not much improvement unless you are prepared to pay serious money.
A 3.9 is putting out approx. 180 BHP, a 4.6 around 240 BHP, neither of which is great if you think about it.
By comparison the (Jag derived) SC 4.2 in my L322 RR is allegedly around 400 BHP.
Having said all that, don't discount fitting any RV8, they work very well in any Defender & always put a smile on my face