I have no experience with the fuel injected 3F but if it's a 4.5l 1FZ-FE motor then yes, it's entirely expected behaviour.
You have described one of the symptoms. This is caused by water in the distributor. The distributor is relatively well sealed, however, Toyota decided it was so well sealed, it didn't breath and condensation was a problem in colder climates. In their infinite wisdom, they drilled a hole in the back of the distributor (aluminium body). Some seal it off completely with silicon, however I inserted a small rubber gromet to reduce the size of the hole to about 1/2 mm. This completely cured the problem.
In any case, it's relatively straight forward to dry it out. Remove the distributor cap by undoing the 3 bolts (I think 10mm) and dry it out. No need to pull plug leads from the distributor. While you're at it, may as well chip off the build up on the terminals with a small screw driver. Also, don't be tempted to file the black carbon from the rotor button. It's specially coated unlike most rotor buttons.
Another hassle with water is that the motor may run fine until about 2,200 rpm and then quit. Runs again as the revs fall to around 1,800 rpm. This indicates water ingress in the plugs near the throttle position sensor. Again from memory, pull the 3 plugs in that area and dry them out. Electrical contact cleaner is excellent for this.
As for water proofing for deep crossings, this can be done. I was faced with crossing the Jardine river some years ago in my last 80. I coated the plugs described with thick Moreys grease (it's really thick. The stuff you can't pump through a grease gun) and ran a bead of grease around the base of the distributor cap. I then went crazy with a can of silicon spray on anything and everything under the hood.
The Jardine's too wide to snatch a vehicle out if you stop and there is an ever present threat of crocodiles, so climbing out the window to work with any recovery gear is out of the question.