Check engine and VTM-4 light on and engine missing in 2004 Honda Pilot

I have tried replacing coils in cylinders 1 and 5, as they showed up as having misfires multiple times. Plugs have also been replaced.

There is a nice write up on the problem you are probably having here:

Thanks. That is helpful. The Honda dealership told me today that my injectors are clogged and I need to replace all 6 of them. I will ask them about the idle speed control valve.

It could be clogged or partially clogged injectors. If the car runs and drives without much trouble, try running a tank of gas with a can of Seafoam or Techron additive to clean the injectors. It’s a long shot but worth a try considering the price of new injectors.

If the engine is missing I suggest you look for it. Once you find it and put it back your problems should go away.

Just kidding. I couldn’t resist.

Hold the phone! The dealer wants to change 6 fuel injectors because 2 (#1 and #5) may be faulty?! This is wrong for several reasons: the dealer’s people aren’t/can’t/won/t properly diagnose the problem with your vehicle; there is no acceptable reason to change 6 fuel injectors, instead of just two. I suspect the dealer’s people of, at least, incompetence.
Take your Honda to an independent shop for PROPER diagnostics. IF the fuel injectors are partially plugged, they can determine that, and do a pressure cleaning of all the fuel injectors. The pressure cleaning is often effective; if not, Auto Zone Auto Auto Parts has the fuel injectors for $55 dollars. Whichever the repair shop uses, the fuel injectors shouldn’t cost you more than $100 each, IF needed.