Headers hitting idler arm

The height of your centerlink (and thus your inner tie rod ends) is determined by the idler and pitman arms. So, unless your idler arm was totally wonky, the suspension rebuild in your case would have minimal effect on clearance. More likely would be your motor mounts going soft and spongy with age, allowing the engine to sit lower. Since you feel your pan clearance is also not what it should be, that is where I would start. Throw some new mounts in it and see where you are- if still not great, add a couple of shims. Just don't get carried away with shimming- remember, every quarter inch you raise the engine is a quarter inch less hood clearance on the top side.