I placed an order for SCSTs at the end of December and discussed most of these options with Jim prior to doing so. I also ruled out the HT2-TL due to WAF issues.
I went with the 1" MDF, since there was no upcharge over the 3/4". Jim did not feel there is much difference in sound between the two, or even with going to bamboo, with the transmission-line design.
I went with the "standard" Solen polypropylene caps. Jim said he makes a point to A/B speakers they build with upgraded caps against ones with the standard caps before shipping them out, and that he still uses the standard caps in his personal speakers.
Presumably you will get this same info from Jim, but since he's on the road there might me a delay, I don't know.
As far as finish, I'm getting Fumed Eucalyptus:
http://www.certainlywood.com/detail.cfm?ID=5313I thought it looks very interesting, but it is much less expensive than the burl options, for example.