Have a 67 Malibu with a small block & auto trans. The headers came with the car, don't know the brand but appear to be 1 5/8 full length primaries with 3" collectors. All suspension parts are new; the engine mounts and body mounts are original. I had to dimple the number 7 primary (driver's side, third pipe from the front)to (barely) clear the rear bracket for the front lower control arm. It is entirely possible that these headers are either not designed for the car or that they are an older design. Is it common to have clearance problems in this area? Can anyone recommend a specific brand that will allow more clearance?

That is pretty common. Most headers for older cars are made to fit several different models. In fact, IIRC, Hooker's have the same part number for Camaro, Chevelle, and some other cars. On mine (Dynomax) I had to the cross shaft bolts for clearance.

The cross shaft bolts are not an issue - they are on the upper control arm. My problem is at the lower control arm bracket.

Hooker Competition, Not Super Competition, fit my 67 just fine, SB 4 spd.