There are a number of factors that affect the final product, some of which you've mentioned.
Race bonuses and any bonuses you may have applied during the game set-up; tech advances ("Reinforced Hull and Hardened Hull both have HP bonuses to apply); galactic resources (which add to Att/Def numbers); military starbase bonuses; and Trade Goods (Xinathium Hull Plating, for instance).
There are speed bonuses: "Gravity Accelerators", for instance; and there are planetary bonuses you may have gotten for an individual planet (given at the moral "choice" screen when you colonized it), or via tile improvements (like the various Hyperion builds).
I would suggest you set your designs to kick in at various benchmark techs....and be very careful of size requirements (you don't want to be waiting for a design to become available...RIGHT NOW!!!)....when you have several techs yet to research.
It took me quite awhile to arrange my designs to become available at a constant flow as I finished tech research, so it may take a little trial and error to do the same.