I also have an 06 with similar thumping (though only/mostly on the passenger side — and it’s not the washer fluid reservoir) even after replacing the stabilizer bar links and the front stabilizer bar bushings. When getting my tires replaced, I was told that the control arm bushings needed replacing but the tire shop said that those worn out control arm bushings wouldn’t cause any thumping noises.
Your fix sounds pretty involved. How hard was it and how long did it take you? Any photos or diagrams of the metal on metal contact point?
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I'll attach photos here if I can or you can PM me.
It took better than a day, but that includes replacing the rack and pinion steering assembly. Frankly, if I hadn't had to replace the leaking rack, I wouldn't have discovered the engine-frame/subframe interference. It's not a glaring conflict until you spot the dimple and its cause, then you realize the insulator is all but useless, and even the struts' absorption is compromised as bumps are partly sent directly into the cabin as well at the control arm pivot point.
It's an engineering flaw, made worse over time as the insulators are compressed and light contact hardens. You can see the original dent framed by blue tape pcs and the taped part of the (now lowered) control arm at point of contact. The second pic shows the frame corner with recess made with rotory-tool grindstone and a related rounding of the control arm bracket below. In addition to the frame mods, I also added rubber to the frame above the upper insulators, which are noticeably compressed compared to new ones in a vendor pic. My photo shows a large 1/16" rubber washer, but I've since added two more for 3/16" added lift. I cut these myself out of a sheet of 70-durometer rubber from Grainger, but you could use gasket material if.it's hard enough. I also added a fender washer and two rubber washers were the small stay/stiffener arm connects the engine frame to the cabin.
You can look up YouTube videos for rack and pinion replacement for RL, Pilot, or Odessey to see the procedure or reply here or via PM with questions.
I don't think a dealer will do this, because it's not in the manual and a frame mod, however minor, would be frowned upon by Honda engineers, out of reluctance to admit such a simple error as likely as any other reason. I do recall reading in the marketing for the Gen-2 RL that the subframe mounts had been redesigned for a quieter ride (no mention of eliminating metal-to-metal contact betw engine cradle and cabin subframe (D'OH!)