On most of the conquests that come with C3C the amount of bonus terrain tiles is much greater than in the epic games. Is there a way to increase the frequency of bonuses appearing without making a custom map? Just make a mod that has increased total bonuses for random maps of all kinds?

You can't change the appearance ratio of bonus resources, but you can add multiples of them. Since they aren't required to build things, unlike the strategy resources, you could have 2 of each bonus resource and wouldn't have to worry about there being 2 separate resources to acquire. However adding more types of resources reduces the total number of resources on the map, so adding a lot more would not be beneficial.

I am not sure I fully understand what your saying. I want to make a mod that will add stone, pearls, jade, and wool to my game. None are tradable lux, or res. Just simple tile bonuses like fish and cattle. But I want this to increase the total number of bonuses. So more fun stuff appears on the map total. Are you saying this isn't possible?

Followup:

Will adding these bonuses change the amount of lux and res items? Or are those independant?

To get many bonus resources (only them), you must place them "by hand" and place many, many of them. But I think you're right about that the number of bonuses increase when you add new one's. I don't know if or how the placement of bonus resources resources will affect strategic/lux resource placements.

I suggest you experiment with this, and then you must tell us what you find out. ;)