Honda recalls cars for frame rust
Honda recalls CR-Vs from 2007....
Honda recalls 564,000 CR-V SUVs due to possible rusting on suspension system - CBS News
Honda recalls CR-Vs in cold states to fix frame rust problem | AP News
For those thinking of changing the ATF, I wrote up how to do a 100% fluid exchange (not a flush and not a simple drain and fill). There should be a link in my signature. Hope you find it helpful.
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Congrats on finding a good frame! As for plugs I ended up changing the boots too since they were cracked. I have a write-up with pics. The link is in my signature.
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running rough? could be anything but check your plugs and your ignition coils. for me I found some dried coil boots. also fluid film your underbody to keep the rust away.
not sure if you implied that you are going to do it yourself. if you are, here is a write up ATF Exchange (using the cooling line) - Toyota 4Runner Forum - Largest 4Runner Forum