Not in a Bonne, but it is a S2 L36. Recently changed the lower and upper intake gaskets, and ever since the change, when I accelerate under load, the engine stutters/bogs down like it'* trying to stall, kind of like a vacuum leak. I've noticed it only really seems to do it when the TC is locked, because while it'* doing it, if I tap the brake pedal to unlock the TC, the stuttering stops and RPM climbs. I'm trying to narrow the problem down as much as possible. I've checked all sensor connections and vacuum lines, all look good. Tomorrow I'm checking the spark plugs.

Just checking to see if anybody has any ideas or has experienced the same issue.

Pull the oil cap off at idle. Is it sucking like a bad dog? If so, put the other o-ring back in the PCV. Either on the valve or on the cover, whichever one is missing.

Plugs were fine, and I popped the oil cap off and stuck my hand over the port. No sucking at all. Any more ideas?

Have you checked plug wire /coil routing? Also, plug wires can be broken internally (especially the rear bank) when removing them from the plugs. If you removed the plugs/wires to do the work and did not install new wires, that could be the problem.

(Image copied from "firing order?" post located using search feature at top of page - thanks, harofreak.)
This image is from an L67, but your L36 routing/coils are set up the same.