As Chris said, you don't have to put the larger TBI on but if you're looking for performance, I'd advise you to at least have the intake bored out to 4.3 specs. Even if you just use the 2.8 TBI, this leaves you the option of bolting on the larger TBI later.
You will need to upgrade to 4.3 injectors as stated or the rig will 'lean surge' when cold. If you use 2.8 injectors, once in Closed Loop it'll run better but will probably be down on power 'cause the 2.8 injectors can't flow enough.
You can 'cheat' and jack up the fuel pressure on the 2.8 but this requires disassembly of the top half of the injector pod, the part containing the fuel pressure regulator. Then you take a pair of pump pliers or Vise Grips to the ring at the bottom of the regulator and twist to snap the spot welds holding it in place. Then you can tighten up the pressure on the spring to increase fuel pressure and this may work well enough to where you won't need to change injectors out.
You don't need to change the ECM or anything else if you take care of the TBI issues. Make sure all the original smog equipment is functional including EGR.
Besides the starter mods, one other issue the mechanic should address is fitment of the oil filter adapter. There will probably be an interfering casting on the block that needs to be cut/ground away to allow the Isuzu adapter to fit.
They should also be aware that only 2 bolt holes per motor mount line up. This is OK, nobody's motor that I know of has fallen out yet!!!
Another detail, make sure they put in a new tranny input shaft pilot bushing (if manual trans). This bushing is Oilite-type and must not be assembled with any grease on the pilot shaft.
Also recommend you use a 3.1 clutch out of a Rodeo 4WD. Must be a 4WD/MUA5 tranny as the 2WD versions use Borg-Warner trans. Surfacing the 2.8 flywheel is mandatory if you do this, as the 3.1 clutch disc is larger diameter. It definitely has a better feel than the 2.8, as I can attest by use of a 3.1 clutch in my 'stroker' project.
Make sure they have observed that the lifters auto-rotate when the crank is turned. 3.4's are notorious for lifter/cam lobe wear and if each lifter doesn't rotate the cam/lifter are shot. Use the HT 3.4 cam if you replace, this also requires use of matching valve springs/retainers.
Anyway, I think these are the high points. If I think of anything else I'll post later.........ed