Sorry, it's unclear what you're trying to do here, so I can not really give you a clear answer.
As a starting point though, the searches return issues based on criteria, so you can easily run a search for "Issues in project A or Project B" and then include the custom fields in the output. And you could also add "and custom field = X, Y or Z" to narrow it down more. The issue navigator allows you to sort by any of the columns.
So, it is possible to do some comparisons, but I think you are looking for more than that.
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