This is a "how to" for solving a problem the pisses-off Honda Civic, Accord, and Acura owners whenever they have to disconnect/reinstall the shifter linkage to work on their clutch or transmission. I thought I'd offer what I learned back to the forum that helped me do the transmission swap.
Here's a guy with the "destroy-the-pin-forever-by-drilling-it-out-and-then-replacing-it-with-a-bolt-not-specified" solution:
As this guy discovered removing this pin while laying on the ground, like I also was recently, is a PITA that can leave you stuck for hours or longer. His solution is clever but the boot is not covering the input shaft as completely as it is supposed to. OEM calls for the pin to be covered by the boot. Keeps the road gunk out. Here's a better way:
TO REMOVE THE PIN
Use a pin punch tool such as this below. The Honda service manual calls for an 8mm punch, but I found removal easier with a 6.9mm one because it was less likely to hit the sides of the linkage instead of the pin. I bought a set at Home Depot for about $12, I think. I'll bet that's less than the price of the pin itself, and you won't have to wait for Honda to deliver it to the dealership. Removal takes firm, confident strokes. It will at first likely move only a little at a time. Pin punches:
And I used this guy's work as a model for how to hit the pin (note his work on linkage beginning at 5:00):
TO REINSTALL THE PIN
The following simple method worked for me while lying under the car, using the same pin that I had removed, still in good shape.
(1) You'll need a nail thin enough to thread through the spring pin with room to spare and long enough to protrude from the top of the linkage after you thread it through the pin and the hole in the linkage that the pin will go into. The head of the nail must be as wide as the diameter of the pin itself (about 8mm).
(2) You'll need a small piece of cork, shaved maybe from a wine cork.
(3) Thread the nail through the pin and the linkage, hold it there, and poke the cork onto the top of the nail on the top of the shifter linkage.
(4) The pin and nail should be able to suspend themselves comfortably and kinda firmly in place without you holding them.
(5) Wack the nail head with good confident strokes until the pin starts to thread in. The nail will probably drop to the ground after a few strokes, leaving the pin started on its journey into the shifter linkage...
This will work in a couple minutes, while lying on the ground, saving you a pin, a parts trip, and days of waiting for the delivery.