I only speak from previous experience of the kernel.dll CTD, which is memory related. I've not had a kernel error show up if say I save in port or right next to another ship at sea, these normally cite just sh3.exe as the cause. If the OP just said 'I'm getting a CTD' and nothing else, I'd suggest the things you have before going into patches and boot edits.
Mileage will vary depending on system specs, granted, but it worked for me when I experimented with both FMInteriors and MFM, although I've yet to try with both simultaneously, somehow I don't think it'd work.
At the end of the day, you can try. With backups done properly you won't screw things up.
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The owl and the pussycat went to sea in a beautiful pea-green boat.
It only took one T1 eel to convince that boat not to float.
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