RAM - Yes you can up it to 8GB, check for the Samsung 4GB modules on ebay, they are super cheap and easy to find.
CPU - Don't waste your time with the CPU, there will be little benefit in performance by replacing the CPU with a slightly faster Core 2, in fact, you probably won't notice the difference, so I would say it's not a very good cost-performance benefit ratio.
BIOS flash chip - That's going to be a significant pain to replace, I would advise leaving it alone.
Bluray drive - I believe there is a slim bluray drive for the T400, search on ebay for it.
3G modem - Why would you go through the trouble of librebooting a device only to add a severe privacy invasive hardware that requires nonfree firmware in order to function? Best to get a mobile hotspot of some kind.
Larger capacity battery - Check ebay, tons of batteries, although given the age of the T400, batteries can be hit or miss sometimes.
Docking station of some kind - There is a docking station for the T400, again check ebay they are dirt cheap.
The minifree machine comes with a nice wifi card preinstalled - Are you sure about this? If it's the AR9285 then it's going to be prone to overheating issues. Upgrade to an AR9380.
I'd also like to know if anyone has ideas on how to use the AMD GPU with free software - Not possible with libreboot, you would need coreboot with seabios payload.
Final question - does anyone know of what is the most powerful and modern thinkpad that can reliably run coreboot? - Look into the T430 with coreboot + me_cleaner.
One other note from your other comment. Libreboot is not a fork of coreboot, it's a blob-free distribution of coreboot.
Hope this helps.