Slightly OT: Mazda Protege engine noise

I know it's not a Mazda group, but it's a pretty bright lot in here, and I doubt this issue is really Mazda-specific.
We just completed an engine swap (1.8l four, auto, EFI) in my buddy's
'93 Protege, and while the new engine (well, used, from a wrecker) fired right up and seems to run smoothly, there are some bad noises. One is a steady clicking that appears to be one of the injectors. That one doesn't worry us so much, but what does is the rattling/clanking sound that SEEMS to be coming from the intake manifold and/or throttle body. It almost sounds like something lose banging around, as it's steady in time with the engine at idle, and starts after the engine starts to warm, gets worse as it warms up, and seems to go away when we rev.
Everything bolted to the back of the engine seems tight and solid; there doesn't appear to be any "outside" source of the noise. We're wondering if it might be an intake valve and the noise is just travelling up the manifold such that it seems to come from there.
Any other ideas of what to look at? Any help is appreciated...
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