As far as installing the coils go buy the gm terminal ends from summit and a crimp tool. I took my NGK wire set I was using on my car, and delicately removed the rubber boot with a razor, careful to not damage the actual wire at all on the end that goes to the coils and delicately uncrimped the terminal end from the wire. Now use a pair of needle nose pliers to get things started and the crimp tool to finish off the crimp of the new terminal end. Now install the new rubber boot. It helps to have some silicone lubricant spray as well to clean the wires and ease the install of the boots. Also pay attention to the orientation of the boot. The coil boot should point in the opposite direction of the spark plug boot so you don't have to twist the wire when you install it on the car. It should point in the same direction as the old boot so an easy way to do this is just mark on the wire which way the old boot is pointing before removing it. Wires came out great and the resistance is identical from before I swapped over the ends.
http://store.summitracing.com/partd...400105+4294756594+4294844024+115&autoview=sku
However if the shop is saying your plug wires are the reason certain cylinders have no spark, they are most likely wrong about that if the car ran fine before they put in the MSD.
To wire in the trigger wires for the coils just cut off the coil connectors and install spades. Make sure the two wires that fired 1 and 6 are still connected to a coil that the 1 and 6 plug wires go to. 3-4 still fire 3-4 and 2-5 still fire 2-5. All that is left is to make a mounting bracket for them then.
Very straight forward job and the car will run off these coils just fine if you ever remove the msd from the system. Its less than $150 for new better than stock coil pack, way cheaper than a new toyota one and way better than a used 20 year old one.