Everyone is different but here's what I do. I use a 12 lb test line tied to a barrel swivel with a 3/4 oz egg sinker above the swivel. Below this is about 18-24 inches of 10 lb test fluorocarbon line. The hook is a small number 4 Gamakatsu Octopus or a Mustad Wacky worm hook. I put the hook through the shad's bottom lip. I never hook both lips as it seems to kill the shad. Perch I hook through both lips.
Once ID a school of fish, I drop the shad down about two feet above them. I set my drag extremely loose, as I use spinning reels and want them to act like bait casters and let the fish have lots of line when he grabs the shad. I put the rod in a rod holder and start working on the second pole. The goal here is to allow a smaller striper to get the shad totally in his mouth before getting resistance. With bigger fish this is not an issue.
Usually, I never get the second pole in the water if the fish I've marked are actually stripers. Line will scream out at a high rate, I take the rod out of the rod holder and give the drag a half turn and set the hook, although the striper probably is already hooked. Typically, they will run out 100 yards or so and have a couple short runs at the boat before I net them and put them in the ice.
If I get two rods in the water I either spot lock if there is wind or put the boat in a very small circle at less than 1 MPH. If the fish don't take the shad after 5-10 minutes I go somewhere else. it's been my experience with shad that stripers will take them instantly regardless of whether or not they are hungry.
As for Perch in a live well, I think you'll have no trouble. I've had over a dozen in a cool bubbles minnow bucket with a small aerator. perch will last but shad will get red nose, make a lot of foam and begin to die. Before I got my shad tank I would use two 5 gallon buckets and try to keep a half dozen shad alive by swapping them back and forth. A lot of trouble but shad die fast.
Perch will likely work at PK because the large number of small stripers and the huge sandbass schools have lowered the shad population from last year.