I have a 1964 Fairlane with a 289 and C4. The car has had a 6 cylinder and a few V8's in the past for power. There has been two sets of modified headers in this car. They were 1.5" primaries into 3" collectors. This is the last set up that was a little tight but all the header bolts could be reached.
That is 2.5" pipes into a 3" exhaust. It worked well but then I added AFR heads and a larger VOO DOO cam. The headers restricted the ports in the heads. The engine compartment has been modified to fit 1966 and later headers but that is another story. The 1.5" headers were Dynomax. I bought 6901 Hookers to get the larger 1.625 tubes and a little more equal length. Remember these are 1966 on up headers on a 1964 so this is not a Hooker fitment problem.
As you can see the headers do not align with the cross member. The old ones didn't either but these collectors are longer so they almost hit. I may have gotten by but I have the tools to make it better. First lets take some measurements. Measure to all parts and take notes. I had an emergency brake cable that also needed clearance. Look at it awhile and picture what to do.
The next step is to secure the points that will not change. That would be the side mounting points and the transmission mount. You can weld it down or make a fixture to hold it securely.
These are some readily available parts. It is strut, threaded rod, and perforated angle. This is what I made but you can use what you have. Just make sure the points are secure enough to not move.
Now that we have a secure mount it is time to mark where material needs to be removed. I cut this with a portable band saw but a cut off wheel or reciprocating saw will work fine.
The pieces were mad with flat bar stock. It needs to be bent to a radius that will work. Here is a 3" pipe in the vise with the metal bent over it.
Needed a tighter bend on one end so I used a smaller pipe cap.
Now that the metal is bent it is time to test it in the fixture. Since the mounting points are secure we can test the fit one at a time. I would suggest tacking the parts one at a time and not final weld them until all are in place.
Next are the side or vertical pieces. Use paper or card board and label all the pieces. This is not Ford Motor Company so they will not all be the same. Accept that and recheck all the parts.
If all the pieces of the puzzle are in place it is time to weld. Weld all you can while it is in the fixture. That way when you put it back in it will fit just like the original.
Almost done. My car gets used and abused. I don't want to break this part. If in doubt weld in a second piece of metal at the vertical cuts. The edge of my part was getting narrow so I felt it was worth the time.

Time to see if it fits and offers more clearance. Well it looks like I can get my socket in there now to tighten those bolts. Nothing will be hitting and rattling either.

The exhaust is finished with 2.5" pipes into a 3" Y pipe with a flex connector into a Heart Throb Velocity muffler. That is Krylon BBQ Grill paint on the exhaust. 1200 degrees and half the price of header paint. Not sure if it will hold up on headers but it will not burn off at this point. I have used it for years.
So what is the point?
I might have squeaked by but now it is the way I want and every thing fits. The idea of this is to show that with basic tools you can make things that you dream. There was a point I would not have done this. I want to encourage you to try some of these ideas so you get the itch or the confidence to do it your self. Remember to use paper to test fit your pieces, anchor parts that you want to modify and bolt back in and have them fit, and remember you can do it.