Run it for a bunch, Shut it down,
Go back 5-10 minutes later and engine sounds clattery, seems like an extra "thumping" coming from the intake like a valve stuck open.
Runs like that for 30 seconds or so on start then sound goes away.
Poor description I know, but would this be something like a leaky or collapsed valve lifter?
1997 1.9 AAZ
Could be related to oil pressure finally up after a hot run. Sometimes it takes pressure to build and oil disperses under pressure.
That comment on clattery makes me also think of injectors. They sound nasty if they are stuck or something is in them.
Only providing to comments as that is my two cents.
if, during "thumping" its actually huffing/puffing back up intake; im almost considering going retro back to the time when older engines were going, oh yea like ours, but older than your newer '97. it could be a sticking lifter. aside from swapping out, one old school trick, get a good bottle or two of engine (oil) flush. heat car up, by driving, put bottle in or two, oh yea shut down hot motor first, restart, hot, no delay, fast idle for 20 min or so, reving some, a little, let idle, fast idle @about 2k rpm, no more, vary some. drain(oil), new oil. usually it makes sense to use a thinner oil, like a 5w. the sticking can be from a dirty motor, or thick oil can stick a lifter. if it is a lifter. sometimes a flush(oil) can clear out a sticky lifter.