I'm not convinced it's a "mixture of similes". I can't find any relevant references to like a kipper prior to about 1970, and I think when it did come in about then, it started as South London slang.
So I'm inclined to credit the explanation given here, that it's a reference to the the extra wide tie called the 'kipper' that became popular around then. Thus called partly because the original designer was Michael Fish, and partly because of the tie's shape.
On the metaphorical allusion to kippers the foodstuff, I'd note that they're pretty unrecognisable as "fish" once they've been split and smoked. They've been well and truly done over.
Also note that to have a stitch on someone was (now obsolete) British slang for to bear a grudge. Which is probably where the later slang stitch someone up came from (it means to "frame" someone - falsely make it appear they're guilty).
OP's more general definition (to trick someone) is increasingly common lately, but I think with or without "kipper", most usages still relate to being (usually falsely) made to appear guilty.