I've never changed the timing belt in the VXs, so this is just a SWAG:

1. The OHCs are "direct attack" or whatever. The intake/exhaust cams are phased off of a single cog on each side. One whole bank of your engine would be out of time, this would explain the backfiring (exhaust valves open at detonation) and the misfire in cylinders 1 and 3 (same side).

2. If you simply took out (a good, whole) belt, and put in another, why would you have had to rotate the camshaft cog(s) at all? As long as the crank didn't rotate (in the absence of a belt), the camshafts and crank/piston arrangement should have went unchanged.

3. It's apparent that the #2 piston was not at TDC when the belt was originally removed -it's too late to do anything about it. Those timing marks are designed to line up under ONE condition, this eliminates the possibility of installing the belt in a '180 out' configuration.
Remember, during the suck-squish-bang-blow cycle, the #2 piston moves to the top of its travel 2 times. It's possible to locate the #2 piston's uppermost position and STILL be 180* out of phase (in relation to the camshafts' intake/exhaust arrangement). Next time, ensure that the #2 is at TDC AND the marks line up before removing the old belt.

O.K. what to do now:
You can't go any further on your own. Thank Isuzu for building a non-interference engine, because your timing is bonked.
Pretend that you broke the old belt, and take it in to a shop -one that has experience in DOHC V6s.
They will have to locate the correct positions for each of the OHC banks and the crankshaft based off of the firing order and the position of the camshafts' lobes (yes, they will be pulling your valve covers, unless there is a guru there with a fiber optic scope who can look through your oil filler hole (think gynecologist/mechanic) and determine your camshaft orientation).

It sucks that you have to pay some shop to do the work, but hey, your time has value. Think of all of the trial and error work, as well as typing and waiting for responses and it all adds up. AAA and a few (hundred) bucks and it'll be a memory.

RLTW