For anyone looking for more rod holders you can check out www.kayakfishing.com.
Actually, there are some great pictures there that show some huge fish (> 100 pounds) landed in a yak.
The link below is for the rod holders. I have the Scotty Powerlock Rod Holder and I really did like it. It holds a fly rod without any wear and tear and you can troll with it.
One thing that you should consider when outfitting your yak is the positioning of any protruding additions (like a rod holder or paddle clips). This is obviously true with regard to interference with your paddle. However, depending on how you get your yak on top of your vehicle you should be careful that any after factory add-ons will not shear off or be subject to severe stresses during mount/dismount and during travel. Just something to consider. I know that when I put 2 yaks with paddle clips on the roof of my car the tie downs that secure the yaks can stress (and may eventually break) the clips. Then again I mount the 2 yaks side by side on the roof of my Subaru. The roof rack requires you to mash the 2 kayaks together.
I also bought the paddle clips at the same kayakfishing site. They are the CKF paddle clips and I like them. However, they are not great for holding your rod while in transit.