The manual of my Explorer2006 4.0L recommends 87 octane gas. I have been using 90 octane for over 3 month now. Could this cause any problems (in the long run even).
Will using 93 octane cause problems. Should I stick with the recommended 87 gas even though the higher octane gasolines are cleaner and smooth out the ride?
No, on the contrary. The higher octane you use, generally the less the engine suffers, the better fuel economy you get out of it and the smoother it runs. All of which translates into a longer lasting engine. If you also take care of it in other ways as well. I would say that recommendation by ford for the use of 87 octane means don't use anything less.
The best running truck I ever saw was a 1972 ford f100. The owner regularly ran 100 octane, low lead content aviation fuel in it. That engine was CLEAN!