Currently I have a paddle kayak (Jackson Big Tuna). . . . The big question is keeping the downrigger and the fishing line away from my paddle stroke while keeping it all secured.  Next time the kayak's pulled out will be mock-up time.

It's a lot harder to mount a downrigger on a paddle kayak than it is on a pedal kayak, because a kayak paddle and your arms sweep over a lot of the kayak with each paddle stroke.  One option is to buy one of the small and more primitive downriggers such as the Scotty LakeTroller, and find a place to mount it which is out of the way of your paddle stroke.  I showed how I mounted a Scotty LakeTroller on my 13' Trident in a posting at http://www.northwestkayakanglers.com/index.php?topic=11486.0 . I find it real inconvenient to use a downrigger which is mounted in the rear cargo area of a sit-on-top kayak, but that is one location where a larger downrigger can be mounted on a paddle kayak.  Try to position the downrigger's pulley where you can grab the weight and release, or you'll need to use a weight retrieval ring to pull the weight over to you.  Another option you can consider is to mount a larger downrigger right behind one of your hips with an angled mount which positions the boom pointing down at an angle so the pulley is right above the gunwale and out of the way of your paddle and elbows.  If the downrigger is right behind your hip, you can crank it without turning sideways in the kayak seat, if that doesn't hurt your shoulder.

If you like downrigger fishing, consider buying a pedal kayak.  It's a lot easier to mount and operate a downrigger in a pedal kayak.  And you can apply everything you learned when mounting and using a downrigger on your Jackson Big Tuna to mounting a downrigger on the pedal kayak. 

Nice video and nice downrigger setup, Alex B!  Dark Tuna, I have the following additional technique suggestions for using a downrigger on a paddle kayak:

1. When downrigger trolling from a pedal kayak, you have both hands free to operate the downrigger and handle your rod, as shown in AlexB's video.  But when downrigger fishing from a paddle kayak, you need both hands for paddling.  So leave your trolling rod in its rod holder when feeding out fishing line, putting the fishing line in the downrigger release, and lowering the downrigger weight.  Turn on your reel's clicker when lowering your downrigger weight so the line won't go out too fast and create a snarl in your reel, and so the line won't bow out behind you too much underwater.  When the weight reaches the desired depth, leave the rod in its holder and crank on the reel to put tension on the rod and fishing line.  I prefer to do the same thing in a pedal kayak.

2. When downrigger fishing from a pedal kayak, you can keep pedaling forward while you use both hands to feed out fishing line, clip it into your downrigger release, and lower the downrigger weight.  This keeps the fishing line streamed out behind your kayak.  When downrigger fishing from a paddle kayak, you'll need to stop paddling momentarily to do those things.  If there's a big wind, your kayak can get blown over your fishing line during this process, and the line can get tangled in your downrigger cable, downrigger release, or rudder.  So if there's a lot of wind, turn generally downwind before you start streaming out fishing line, so the wind will keep your fishing line streamed out behind you while you mess with your fishing line and fishing pole.  Also, once you get your fishing line streamed out behind you, turn the nose of your kayak slightly towards the side of your kayak on which the line is located to keep the line away from your rudder until you have lowered your weight.  It's a big hassle if you get your fishing line tangled in your rudder when you're away from shore.

3. As AlexB says, ergonomics are important, because when downrigger fishing, you'll be raising and lowering your downrigger weight repeatedly during a day of fishing.  I frequently downrigger troll at depths below 150 feet, which is a lot of cranking.  If your downrigger is located in a place where it stresses your shoulder, back, or other body parts while cranking up the weight and otherwise operating the downrigger, you won't be happy with your downrigger setup.

4. I use braided line on my trolling rods, so I use a Black's downrigger release which is clipped on top of my downrigger weight. I think they work better with braided line than pinch-style releases.

5. Downriggers come with steel cable, and steel cable tends to hum.  If the hum drives you crazy, replace the steel cable with braided downrigger line.  I use Scotty 175 pound low-drag spectra braided downrigger line.

There's a description of a nicely made base for a Scotty Depthmaster which is based on my Cannon downrigger base posted at http://www.norcalkayakanglers.com/index.php?topic=71837.msg816193#msg816193 .  I like the way G-Force used gear track to attach his base to the gunwale, as that is easier than mounting sealed nuts inside the gunwale, like I did.  I also like that G-Force bolted the base for the Scotty Depthmaster to his base, because if he needs to paddle his kayak, that allows him to quickly take the downrigger out of the Scotty base and throw it in a hatch, while leaving his base and the Scotty base attached to his gunwale.  I wish I had bolted the Cannon base onto my base, rather than bolting my Cannon Lake-Troll directly to my base.

It's real easy to mount a downrigger on the current Hobie Outbacks, because you can mount a rectangle of metal or plastic on the pair of gear tracks next to the cockpit, and can bolt the quick-release base for a downrigger to that rectangle.  The picture below shows a downrigger base next to my friend's right elbow.  He went one step fancier and used a rotating downrigger base.

When I swapped out my steel cable for braid I utilized 80 lb. test just in case of the weight hanging up and requiring breaking off the line.  The choice of 80 lb. braid is more of a safety issue for me.

I switched from steel downrigger cable to 200 pound braided downrigger line primarily to reduce the drag from my downrigger and to get rid of the irritating hum produced by a steel downrigger cable, and secondarily so I can cut the line with a knife if I need to.  I don't think it's possible to break an 80 pound braided downrigger line from a kayak.  I typically use 30 pound braided fishing line, and I've never been able to break it from my kayak.  I use lighter leaders, such as 15 or 20 pound leaders, and they always break first, usually after a bit of struggle.  So whether you use 80 pound braided downrigger line or 250 pound braided downrigger line, if you hook your downrigger weight on something and can't pull it off, you'll need to cut the line at the surface, and the 250 pound line won't be any harder to cut than the 80 pound line. The only factor which might encourage me to use 80 pound braided downrigger line is if I did a lot of fishing in areas frequented by whales, and I was concerned that a passing whale might hook my downrigger line, flippng my kayak without warning before I could cut my downrigger line.