[squidtone]

CB
I went through the same thing. I was afraid of cutting up my car. But after looking into it, it seemed to me that it really only matters for very rare cars, or cars that are super low mileage.
Still, you can do this: When you get the shifter porch aligned and trace out the hole you need to cut, just do it carefully (I used a jigsaw and it was super clean cutting) and make the new hole meet up nicely with the automatic shifter cable hole. Save that cutoff piece. It'll weld right back on and with care it'll almost be undetectable if you or subsequent owner want to put it back to automatic.
My 67 was an auto, and it has it's original drivetrain, (and floorpans) but I couldn't bear the thought of keeping it an auto, so I just made sure to keep my little cutout piece of floor pan. I also saved everything else; the trans, lines, line clamps, screws, driveshaft, etc. It all can be swapped back easy some day.
All other mods are pretty tame too....the weld on "Z-bar" tab, steering column clamp (with clutch rod hole and boot). Anyway, all those mods can be taken off if necessary.
Good luck!