Just a quick status update:
I've tried to make most of the patches in netfilter patch-o-matic-ng work with 2.6.12 today. It's amazing how fast the code bit-rots there.
I've also applied tons of cosmetic cleanup fixes, such as %zu and %ti format strings to avoid compiler warnings on 64bit archs.
Now it's time to head back to the PPTP-conntrack-nat port for 2.6.11+. Once that is finished, I'm back to ct_sync work.