Blake,
Still got the engine in pieces? The first thing you need to do is measure everything. Once you have all of those numbers you will know what your current port timing is, compression ratio, head volume, squish band area, rod length... and so on. By knowing where you are beginning than you can "plan" what you want to change. There are a few simple changes you can make to the engine that will affect how the engine runs.
Being a pulling engine, I guess you are looking for torque over RPM This will help you narrow down the list of possible changes you can make. You can PM me if you like.