Since you have now determined that the engine roughness does not go away at higher engine loads, then it very well could be a misfire and removal of the coils for inspection would be a good first place to look.
The individual coils have a bare metal pad which the mounting bolts bear against. This surface can incur surface rusting if any moisture has made its way past the coil covers. I would not be concerned about mild surface rusting if you can clean it up with a 3M abrasive pad or some 300 grit SiC paper. Serious rust may not be a problem; but, may be an indicator that there are more serious problems elsewhere.
The critical area that you want to check is the long nose of the ignition coil that fits over the spark plug terminal. On the end of the nose there is a rubber boot that fits over the sparkplug. If misfires due to flashovers have occurred this is where evidence will first show up along with traces on the surface of the sparkplug porcelain. You can search the web using the term 'carbon tracking on ignition coil' and you will get a number of hits describing the problem. This site has a photo that is probably as good as any:
The inside surface of the rubber boot on the coil nose and the spark plug porcelain should be nice and clean with no tracking of any kind. The nose above the rubber boot should not have any tracking of any kind. If you do have tracking on that hard part of the nose the coil has to go because tracking there is a sign of serious coil problems. For tracking on just the rubber boot, in a pinch, you could try cleaning it with 99% IPA or a zero residue electrical contact cleaner. However, tracking can cause surface damage and cleaning cannot fix that. Any tracking on the coil nose or that rubber boot and the matching sparkplug has to go.
The ignition coil has a rubber gasket on its base where it contacts the spark plug well which should prevent 'stuff' from entering into the spark plug well. If you have signs of water contamination on the nose of the coil it is an indication that the coil base gasket is not sealing. I don't recall seeing the base gasket listed as a separate part so you should plan for replacement of the coil if the base gasket is compromised. When I did my sparkplugs I greased the base gasket liberally with silicon dielectric grease to help insure a good seal. With grease on the gasket it becomes a near air tight seal. When I push the coil into the well the coil tend to pop back out because of the pressurization of the air in the well. That spark plug well should never be getting stuff in it. When replacing the spark plugs or the coil, also grease the spark plug insulator and the inside of that rubber boot. If moisture ever gets into the spark plug well this helps to seal the nose reducing the chances of tracking along the spark plug insulator. Greasing the boot and the plug will also make removal easier in 7 years. Sometimes the rubber boot can bond to the insulator surface making removal harder.
I believe this is the part # for the 6 pack coil kit:
You can search on the web using the part number and you should be able to find the kit from authorized Acura parts vendors for less than $110. Be aware that at one time the kit also included sparkplugs. However, the sparkplugs were the heat range for the C30, not the C32. If you order the kit and by some odd freak of circumstance it has the sparkplugs included with it, don't automatically use the plugs without checking to confirm they are the right heat range.
Since you have a T roof car, I suggest making arrangements to prop up the engine cover and remove the 3 point brace in the engine compartment. You can remove the coil covers and the coils with the brace in place; but, it is a real hassle. You can also R&R the sparkplugs with the brace in place; but, it is a triple hassle and it is very hard to properly torque the plugs with a click type wrench with the brace in place.
When you put the coil covers back on, the coil covers are marked on the inside of the cover to indicate front and rear. The rubber gasket should go along the top edge of the coil cover. No gasket on the bottom edge. When re installing the cover grease the gasket with a little silicon dielectric grease to help it slide into position without coming off the cover.
Your OBDII coils have a 3 pin plug on them and it has a weather tight seal so contamination should not be a problem. Also, voltages are relatively low so you won't be getting flashover here. When removing the coils this plug has a retaining clip which must be pressed to pull the plug out of the coil (you are doing this blind). Even with the clip released the plugs can be a real b**** to get out of the coil because the plug has a little rubber lip seal which likes to stick to the housing. I also lube the plug and its little rubber lip seal with dielectric grease to make removal easier in the future.
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