Here is the issue

 

Yeah, that could be a problem. That's your reverse lockout/column shift linkage.
If you have a column shifter, you can't disconnect that or you'll go nowhere fast. Then you're going to have to figure a way to bend/tweak/shorten the arm and linkage rods so it clears the header.
But, if you have a console shifter, you can then remove that linkage. If you do though, you'll have no reverse lockout (will be able to shift without turning the key). The vertical rod you see connects to an arm on the steering column. You can see it from inside the engine compartment, below the brake master cylinder. With a console shift, that acts as a lockout by not allowing the collar on the steering column (inside the car) from rotating until you turn the key on. When you disconnect that rod from the steering column, you'll want to wire the arm to keep it in the all the way up position. Let it flop down from gravity, and that will keep you from being able to turn the key.

 

Yep, I removed mine back in the 70's when I put headers on. Wonder how somebody was able to have the headers on your car all this time and not be able to shift the trans?

 

Thankfully I had floor shifter. Took her around the block a couple times man is it fast except I couldn't get it to shift into second. I was getting up in the RPMs and the engine cut off. This is endless!