Soft plastic or "jelly" shads have probably overtaken pirks as the most common way to fish for cod from charter boats and kayaks in recent years. There are hundreds of types and prices to buy. I like the Storm Wildeye shads, in 4" and 5" versions, though it must be said they are not the cheapest shads around.
Admittedly this doesn't look pretty, but the fish don't seem to mind! Neither does having the bullet tight against the eye of the lure seem to affect hookups. Initially I was worried this set up would result in the bullet weight fraying the knot and leading to breakages, as you have to put quite a bit of force to get cod up sometimes. But so far, I've not had this issue. This might be because the bullets I use are cast with very fine holes, and so sit above the knot if you tie a tucked half-blood knot and leave a little stub protruding. While this method is quick and easy to tie, if you've got big tides to master in deep water, you'll need to rig your shads differently to use a heavier weight. In that case, you could use what is often termed a drop shot rig for fishing jelly worms and lures as this rig just bounces the lead off the bottom and so is less prone to snagging up when drifting at speed.
The shad below is the 5" version in blue herring. There's a great finish on these with holographic glitter inside the lure, though I'm not sure the cod care that much down there in the depths!
Cod of 5lbs and upwards can give surprisingly good account of themselves on light rods, and I often fish with just a stiffish (casting rated at up to 50g) 7ft spinning rod. However, if you feel there is the risk of hooking something much bigger and not having the backbone to lever the fish up to the surface, you can always stick with the standard 6-12lb or heavier boat rod.
I like to let the shad hit the bottom and then simply jig up and let it fall back. I tend to use as large a jigging motion as possible, and watch for slack line on the drop. If you don't feel the shad bounce your rod tip at the end of the drop phase, then chances are a fish has grabbed it!
Last year shads accounted for most of my cod, and I find they nearly always out fish pirks. However, one handy trick with pirks is that you can use the fast sinking weight of the pirk to fish a set of hokkais above it. Hokkais can be very effective for cod and many other fish, and I've been searching for a way of combining both hokkais and shads. Until recently, I hadn't been able to find a shad with the weight and smallish size that would suit our type of cod fishing. Then I came across these:
pirk replacement at the bottom of a set of hokkais, they might just do an even better job at attracting nearby fish. That huge paddle tail will really send out some vibrations down there in the inky depths, and besides which even quite small cod sometimes have a go at large and heavy pirks.