It started to cough...

I'm not 100% on the configuration of the 4runner V6. ie I'm not sure where the spark plugs are, alternator, dizzy etc.

A Common trick by petrol vehicles in diesel territory (LOL) is to use a rubber glove with the figures cut off over the Dizzy.
Also a bit of CRC around all the leads, coil, dizzy etc before the water will help repel some of it. Silicone can be used lightly around the dizzy, just don't put too much on otherwise you'll never get the bastard off again!

A New set of leads probally wouldn't go a stray if there getting long in the tooth either.

And if the water's getting real deep a Blind over the front grill will also help.

The problem there is the "at speed" bit. Even if you have splash proof fittings and plugs, driving them with force through water wont do them much good.

Check out the dizzy first - That was the root of my problems with water crossings at speed, and she did the same thing- misfiring and stalling at anything below 1500rpm. I found theres some large breather holes in the back of the dizzy. poo them up with blue loc-tite and she's sweet. If theres no ECU or electronic sensors on it, you should be right with any high-temp silicone.

Finito

did some bog holes once in my TD Jackaroo. I did not have a problem, I would presume because I did not have a dizzy. The 80 series Landcruiser did (stock suspension) and so did the hilux 94 model (4 inch lift). They WD40'd the electics under the distributer cap (to make the water disperse better) periodically, still got stuck a couple of times when the fan sprayed water everywhere. Funny to watch them climbing all over the car trying not to get their feet wet in water up to the top of the tyres, but with a quick spray of WD40 the engine started again and away they went.

I'd say it is water in the electrics, under the distributor cap. Check to see it's not cracked too, and try some of the above sealing remedies to keep water out in the first place and you should be right. The other thing you should do (but we don't) is disconnect the radiator fan so it doesn't spray water all over the engine bay when it hits the water, or use a blind, or take a shallower route across.

D-Jack

When you talk about the dizzy, that seems about right. I have replaced the distributer cap and leads a little while ago, so i know they are all right, but when i got my mechanic to tune the car, he mentioned that my dizzy was set very finely, and would probably need replacing if i continued to have troubles. I wish he had just rang me while he did the job and asked me if i wanted a new part! He also told me the distributer shaft was bent (more than acceptable), but as it was an old car, was not worth replaceing! Again, if he had rang me during the job, i would have had him replace it. I'm sure alot of you would replace a faulty part on an old car if you wanted to keep your pride and joy in working order, and not stopping in the middle of a creek!
As for hitting the water at speed, i can assure you it wasn't helter skelter into the unknown, just at a speed that has the water washing over the wheels.
Thanks for that, time to get a new mechanic.