As far as anchoring a yak, the guys in FL, lots of shallow fishing, really swear by "Dick's Stake OutPole".
I could not find them on Eugene's site, but if he does sell them, please buy from him and I apologize.
http://www.captdick.net/StakeOutPole.htm
I know some of them make their own, and some even use PVC as you have done. I think the issue of sticking it down through the scupper (see below) is wear and tear around the scupper hole, which, over time, might require larger stoppers if you use them.
As for anchors. DO NOT ANCHOR A YAK IN MOVING WATER. My yak has an anchor trolley, essentially, two "pulley" type devices attached to fore and aft with "yak cord, running through them in a loop. You tie on your anchor, then let it out, tie off excess, then use the loop to position the anchor either fore, aft, or wherever.
As you will see in the above link, these guys (who I have communicated with and are real yak fishing EXPERTS) are using the pole on their anchor pulley. I would recommend that solution, rather than through the scupper.
Also, You will have a pm shortly.
I have fished yaks for four years now and never felt compelled to anchor, btw.
LLN