I panic just a little (ok a lot) when it's about to go into 4th gear and the RPM dial jumps and flies with a thump and then it's fine. I have found that if I baby the gas pedal before it gets to that point then it shifts smooth.
I've wondered about that clunk as well when I'm coming to a stop, sometimes it feels like someone has bumped me from behind and sometimes it's harder than other times.
Especially with the cold we've had in the Northeast this past week, I try to go out and start it and let it run for about 5 minutes first, but for the first few stop and gos, it does seem to hang in 1st for longer than normal and then it's fine.
I will say that since I have been putting in plus gas, the trans does shift quite a bit smoother than it did with regular gas. Next time I think I'm going to try premium.