How bad did I eff up?

Regarding your intake install, yes, I use silicone over the cork/rubber for the china rails. Downside, expensive can of pressurized can of silicone. Make sure you make the bead close to 1/4" thick. To help with a guide for the intake, cut 2 3/8" bolts so that they stick up about a 1/2" when in the hole, put them one at the rear and one up front on the side of your choice. Aim for one and then the other and let it settle into place.