4m40 up to 96 has a mechanical pump, post 96 has electronic. 4m41 is all electronic and all direct injection with a variable vane turbo. 4m40 is simple as pie the only electronics is the ecu for glow plugs and egr. i would not swap a 4m41 unless you are good with electronics.
The later ones got the VNT,maybe in 2008 and after,up until then they had a plain ole turbo. Only the post 96 pajeros from japan got the EDC pump,most of the rest of the word kept the mechanical injector pump. You can tell the EDC models by the fact they've 16" wheels to accommodate the bigger brake discs. They are an absolute pig to get running right,they find it very hard to idle properly.
The 4m41 would be the one to go for if you've the patience to get it running right,a nice slice more power than the 4m40 which makes it far more drivable. Only thing is you might want to budget getting the injector pump rebuilt into the cost of the conversion. I've the 4m40 and TBH it is a bit under powered even with some power modifications.