Did you check for a broken piston? I"ve heard them knocking in Ford engines i have worked on.
Or even a broken crankshaft? The crank would still turn, even broken, for a short while. But, it would make noise. The engine would run, but not long.
If i were doing it over, I"d do a complete teardown, and have everything checked thoroughly by a competent mechanic, who is "learned" on Ford engines. Not the latest models, those older engines.
Another thing--when you got it all put back together, were you "short" some nuts or bolts? I"ve seen nuts in exhaust manifolds or intakes, that fell in there unnoticed, and when the engine is started up, they soon make their presence known in the engine, by "knocking"! Some otherwise expert mechanics were "felled" by that phenomenon! (Those errant nuts or clips or bolts seem to lay in wait until you quit for the day, then they jump into an area that is closed up, like the intake manifold, and as soon as you start the engine, they slide down on top of the piston, where they soon get pounded into the piston top, to make loud expensive rapping noises!)
by; Rustyj

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