Yeah, it's a new pilot. I checked it against the old one and it looked identical. This trans came out of the same truck, so I figure it's just skill (or lack thereof) on my part, rather than parts fitment.
I will try the trick with the bolts - that's a good idea. I notice the shop manual specifies using alignment pins in those upper holes, so trying to emulate that is probably not a bad idea.
Guess I'll head out with my two year old son to Tacoma Screw!