Problems with this:
1. You can't just tell them it's a diesel when you show up to renew tabs; they have to inspect it and approve of the swap first.
2. Acceptable engines have to be from the same class of vehicle (i.e. no 4bt from a medium-duty donor like a bread truck or an Isuzu from a genset which never had a VIN).
3. Ok, so, that means it has to just be a 'regular' car/truck donor, right? Well, it has to be from the same weight class, too, so no 6BT/Duramax/Powerstrokes/even 6.2/6.5 GM diesels, since those only ever came in 3/4- and 1-ton trucks, never the 1/2 tons which are actually in the same weight class as an FJ60.
4. Donor engine probably has to be unmodified, which probably means no adding a turbo (or bigger turbo).
Very thorough reading of the rules and regs seems to suggest that the only truly legal diesel swaps for a 60 in CA are Mercedes, VW, and some pretty garbage undersized diesels from things like old Chevy LUVs etc.
People have gotten around this, I'm pretty sure by importing rigs that were swapped (and had their fuel changed from 'G' to 'D' in less stringent states), or non-US market rigs that were imported and registered in less stringent states.
Long story short, you might get lucky and get something past the SMOG rep, but a diesel swap is absolutely not the silver bullet to avoid SMOG hassles in CA.