Thank you all for the replies so far!

I do wear padded shorts, the Pearl Izumi Elite Symphony with a 13mm foam pad. I have read in some threads here that more padding isn't necessarily better and now that I realize I definitely need a second pair of shorts I'm in the process of deciding which ones I want to try (thinking the Sugoi RS short or the Giordana FR Carbon Short though I don't particularly love the long inseam).

I'm going to give my saddle (the Selle SMP Strike TRK) the benefit of the doubt as I love the large canal and cushioning of the seat. I'll see how it goes over the next few weeks and hope that my sit bones callous up to the point where shorter rides won't bother me as much.