Toyota Liteace 5K Engine Misfire

[dr. d]

you used a substitute distributor cap!!??
well, if i were me, i would replace the distributor cap. ...i don't have much faith in substitutes for vital parts.. experience.. but check my comment below first.

inspect the no. 3 tower again. check with an ohmmeter, between the tower outside, and the point inside, to see if it is "open".
also, did you actually see the spark, or lack thereof? if not, maybe you should do it. remove the #3 HT from the sparking plug, expose the metal electrode by pulling it out of the rubber insulating cover (don't pull it out of the cover; push it thru the cover!), and position the exposed metal electrode very close" to the engine (metal). crank the engine. a spark should be seen at the end. if none or very weak, there's something wrong with your spark delivery system proximal to the HT cable's end. this may be the distributor cap or the HT cable.
if you have a timing light or gun, clamp the sensor around the #3 HT cable and see if the timing gun's light fires. if it does not, then your #3 HT is "open".
good luck.

...good old troubleshooting... haven't had this much fun in a long time..