If the header is putting out enough heat to soften the rag joint, you could add/fab up heat deflector shield on the under side of the header, or add some heat wrap to the section of the header that is near the joint.

The starter is on the other side of the engine, and the infamous click-click is just from having turned over 1000's of times, though if you have a 6cyl w/headers, the heat will kill a starter.

More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed