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So my questions are:
1) Is there an easier way to get the valve covers off other than the flexible putty knife?
2) Is it worth messing with the heads (regardless of the valve covers) Is there something I should look for to determine this? (Oil in the spark plugs?)
3) Any thing else anyone can think of I'm missing?

1. A rubber mallet did the trick for me.
2. No. Nobody replaces head gaskets as a prophylactic measure. If one was blown, you'd know something was very wrong.
3. Since you're already this far, you might consider replacing two certain little PITA o-rings in the cooling system plumbing. Rubber o-rings can only last so long. I recently had the pleasure of dealing with this...here's the thread.