it'd be quicker to slip in some 1/2" plywood spacers just to check viability than remove the heater unit and mod' the tunnel some more. if you gain the clearance you need just swap in steel spacers and you're done. also you mention the headers will hang lower, that's not the case. the motor is still bolted to the k member the same, all you've done is raise the body by 1/2" up from the k. so in relation to any of the suspension that's close to the ground the headers remain the same.
neil.