Vacuum system problem perhaps. Based on the change in transmission shifts now there as well. I believe there are vacuum feeds to the fuel body/idle tube area. If a line blew off with a backfire for example . Or you accidentally damaged one or disconnected one when in the area working What did you find was your original problem? Where were you working? I do not know anything about the 3.5 litre engine basically other than there are vacuum circuits in the fuel supply system I believe. If you cannot find it easily you might have to employ a shop manual and a mity vac type device. Could be something else of course but the hard transmission shifts change at the same time is a strong indicator.