Firstly, I would have thought that the original Mitsubishi engine would be easier and cheaper to do than a Toyota swap. You would probably find that the 4D56 (or whichever) original engine is perhaps also easier to find than a kabuli 3C or 2L these days....
I would also recommend looking into an engine overhaul a I would think that quality Mitsubishi parts are available at decent prices and its always a good option taking everything into consideration provided this is done properly....
I am not so well versed with the ins and outs of Toyota diesel swaps into Pajeros, but 3C and 2L are good Toyota choices for swaps as far as the engines themselves but good pieces are rather difficult to find nowadays. Between the 3C and 2L, I would think that the 2L would sit in better with the Pajero gear ratios....
Do elaborate on why you want to stick to diesel and particularly the e-diesels?