As far as the injector question if you use the 2.5L wire harness and the 2.5L ECU it should be able to run the engine but you will probably need a tune. You could have picked up some 19lb injectors from an early SVT they would have hooked right up and they go for about $60 used. Then you don't have to splice into every injector wire and worry about shorts later on.
The secondaries or as you refer to it "air plenum" open up at about 3500rpms and give the 2.5L low end torque when shut and the extra air for the top end hp when open. It's cable driven on the later contours so I'm not sure what you will have to do with that. You can gut them but there will be some drivability issues. You could compensate for them if you get a tune.
It doesn't sound like you swapped oil pans. I thought there was an issue with the Sable/Taurus pans which is why everyone swapped on the 2.5L pan and pickup. Wasn't it that it didn't have holes for the transmission bolts down low? You might want to check into that.
Why not just buy the 01+ 3L though? Then the water pump works like these stock one and you don't have to pay $300 for the electric one if that is what you are doing. As far as the water pump mount what do you mean? It bolts right to the head on the 2.5L there is no mount.
Also the 3L timing cover has that huge buldge in it. If that is the cover you are using then I'm surprised it fit in the car.
1999 3.0L Cougar: 220fwhp and 200tq
2003 VW Passat W8 with 4 Motion AWD
http://www.cardomain.com/ride/300644
PM for intrest in 3L SVT Contours, 3L swaps into your current car, Prepped 3L engines, or anything 3L related.