With that rack it will not cause you any issues. I am using and would suggest early mustang long tube headers on that. Years of installing headers on just about everything at a speed shop gives me the idea that these headers would work great for you and they are cheap.
Yes the ones that go back towards mid transmission, not the mid-length or the block huggers. Early mustang would be 64-73. Sand blast off the cheap paint that usually comes on them and paint them with good high temp paint and you should be good. I have headers that are twenty plus years old, the ones on my truck have been on it for about 19 years, they do need new paint because of the sand and salt they use here in the winter.