i didn't thumbs ya doc.
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you know that we're not going to be able to just point you at one component. to many things involved in an engine swap. only help guide you through trouble shooting.
and there are some things we don't know,
what engine??? was this a long block or short block swap??? did the original 200mi run include any stops where you shut it off and started again w/no issues, or just a 200mi???
excuse me if what i post is elementary to you.
but a few things come to mind,
if the idle is incorrectly set, after the cold start cuts off the idle will fluctuate as the ecu will continually try to correct it. this won't show up at rpm. only at idle after warm up.
pcv or egr issue
any vacuum leak associated with the MAP or IAC
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kinda sounds like you may have done this already, but,
depending on the swap, long or short block, i'd do a cursory check on all vacuum related gaskets. intake to head and any components on the throttle body that have a seal/gasket to the intake or passage/port to it. check all SVS's and VSS's for direction and connections.
good thing she starts. if she didn't you'd likely get more codes than are relevant. so,,,,,
i would first clear the ecu of codes,
http://www.autozone.com/autozone/rep...00c152801ccc73
then start it/shut it down and read the codes,
http://www.autozone.com/autozone/rep...1ccc63#hd1-1-1
likely it will point to something listed here, (generic trouble shooting/some components aren't app. like you don't have points and such. ignore those. & i wouldn't think it's fuel pump/filter/fuel return-over pressurization, regulator, T-belt, or valve related as you didn't mention pinging or lack of power)
http://www.autozone.com/autozone/rep...diagnosisId=43
once a faulty component/system code is ID'd, check vacuum routing to the component,
http://www.autozone.com/autozone/rep...00c152801ccc85
testing and vacuum routing for components not related to emissions,
http://www.autozone.com/autozone/rep...00c152801ccc3d
.