To answer your question, yes, a new chain will affect IP timing. You should definitely check it. If it requires adjustment (spec is 24 BTDC I believe, +/- 1.5?) you may want to adjust to the far side of spec advanced (25.0-25.5 ?) to pick up a smidge of MPG. Just don't go beyond spec, or you'll get excess smoking at high RPM's. (Ask how I know.
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BTW, thanks for relaying the experience - I need to replace the chain in one of my cars (stretched 4 deg.), and this is giving me some motivation to finally do it. Just curious, how bad were your original chains (degrees stretched), and how many miles were on them?
Best regards,