I have had mine apart a few times over the years. I've always had clearance issues at the rear valve cover corner, the A/C pipes on the firewall, and the top of the transmission housing where the connector is. Best bet is to hook everything up loosely, get some wood shims like you'd use around the house. Jam them in between your two rough spots, the pressure will keep things where you want it as you bolt it down. Good luck!