Just assume that it's coming in through 43 and 3/4 gaps that you didn't know you had. Then fix all 54 of them and then 79% of your exhaust fumes will be history.
On a more serious note though, verify that the rear corners of the hard top are full sealed, including the stake pockets. Do you have the stake pocket braces on the top, or did you leave them off? If off, did you fill the bolt holes? Remember that the lower part of the stake pocket is open to the ground all the way past the tail lights.
Also, if this is an original and unmolested body, your rear corner vertical seams might be leaky. Mine actually leaked water every time it rained so I had puddles in both corners and I could watch it bubbling through the inside. And this is when the truck was only five years old, so the factory seam sealer left something to be desired. I filled it with RTV and never looked back.
Basically, if it can leak water, it can leak fumes. Even in a non-critical spot like the side of the body.
The lift-gate as it seals along the top of the tail-gate is a culprit. So are the side and bottom seals of the tail-gate.
As are the seat and seat belt holes under carpet, as are any and every small drilled hole that was not sealed up previously and no longer has anything screwed into it.
Add two or three "all-of-the-aboves" to the mix, and you have your list of potential leaks.
paul