It is safest to make a stock image first, test it, and make sure you have everything working. Then make changes. Otherwise you don't know if something went wrong because of your changes, or because of the builder in general.
There was just a recent thread where I explained the various ways to tweak the kernel options (e.g. EXTRA_OPTIONS in pfsense-build.conf) and I updated the doc here:
http://devwiki.pfsense.org/BuildTimeOptions
What you want to do can be accomplished by just adding one line to your pfsense-build.conf once you have made a good ISO.
I mentioned the path to the resulting kernels in a previous post in this thread already.