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>cvsup ports/src etc .. goto /usr/ports .. portupgrade -aDk -m BATCH=yes ... 
>then /usr/src .. make buildworld && make installworld 
>then /usr/src/sys/i386/conf .. config kernel file and go from there.
>
>  
>
As fas as I can remember, correct procedure for base system upgrade is:

cd /usr/src
make buildword
make buildkernel KERNCONF=your_conf
make installkernel KERNCONF=your_conf
reboot to single user
mount -a
cd /usr/src
make installworld
mergemaster
reboot
Building kernel and modules not with
  "make buildkernel ; make installkernel "
may not work.
Also make sure that you are not using too aggresive optimizations.