Intake Mounting Bolts:
Inspect the intake mounting bolts for distortion at the threads as well as the Allen socket in the head.
Previous over-tightening or misaligned wrenches can ruin these bolt's ability to be retightened properly.

You can replace the bolts with grade 8 or stainless ones from a hardware store.
There is only 6-10 ft-lbs on these bolts so shear strength is not an issue.
Also consider replacing the rear / slotted end bolts with hex bolts instead.
This will make these easier to work with during installation of the intake.
There is not enough room on the carb side holes for a hex bolt due to the small clearance between the intake body and hole.

Stock mounting bolts replaced with stainless, rear bolts changed to hex head. 1)

Flanges:
Double check flange placement before tightening them.
The flanges are directional. There is a letter stamped on each flange for (F) - front or (R) - rear placement.
There is a mounting hole on one side and a mounting slot on the other.
The slot goes toward the 'tight side' between the cylinders or otherwise toward the left side of the bike.