Probably pay close attention to all of the factory plugs/wires associated with R&R the engine. If something small escaped notice then that could be causing it.
More importantly, checking gaskets for leakage will be difficult, but the manifold, TB and PCV system or anywhere that unmetered air can enter the engine needs to be checked as well.
Former owner of '99 CSVT - Silver #222/2760
356/334 wHP/TQ at 10psi on pump gas!
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'05 Volvo S40 Turbo 5 AWD with 6spd, Passion Red
'06 Mazda5 Touring, 5spd,MTX, Black
