If you are working on a 6G74, 3.5L, then let's try this:
The firing order you listed is not correct for this engine. (you didn't post the specific year) This picture shows the coil locations on the newer models, but the firing order is the same.
If I recall correctly, If you have a distributor ignition, then at TDC, the rotor should point roughly to the firewall and actually be under the #2 plug wire tower.
Edit: just looked closely at your picture, of course you don't have a distributor! (duh) When I pull the upper intake, I always leave the coils in place. Many folks simply number the plug wire with white out or similar marker. The coil numbers are stamped on the intake, and the coil leads typically are the correct length to fit the coil. Since you've replaced everything, simply trace each lead from the cylinder in the picture manually all the way back to the correct coil number and you should be good to go.
Other issues could be vacuum leak at intake gasket, but I re-use them if they are good, vacuum lines, missed an emission plug somewhere on the harness?