Oh, oh! I ran into this problem when taking the old poppets out:
I had three of the clips breaks off, locking the poppet into place in the lower plenum's intake ports. Using a thin, and I mean *thin* pair of needle nose pliers, reach into the port along the side where the "ear" for the retainer broke off and grasp what's left. It takes just a firm tug to break the rest of the ear and the retaining tab off on that side. Then using the side of pliers' nose as a brace, I pushed on the remaining, intact tab and was able to wiggle the poppet out of the socket eassily. When putting the new ones in, seat the new injector assembly first after installing the fuel lines. Install the fuel lines first so you can work out the routing of the poppets on the driver's side with a bit of ease. Contrary to belief however, it is not important which order they go in, as the system is batch fired. However, the varying length of the injector pigtail tubing will define where the injector goes. Remember, no sharp bends or kinks and you will be alright. One of my injector lines indeed have to go over the fuel lines, as this was the only way it would go without any rubbing which would lead to pre-mature failure.
I figured what the heck, while I was in there and did what you did, replaced cap and rotor and also took off my EGR to clean it up thoroughly and put it back in. It was sticking due to carbon build up brought on by my regulator leaking. It also fouled out the #4 plug. Though she started up and idles much better, it still loped because of that. A quick replacement with a fresh plug took care of all of it. It's a very satisfying job when it comes together and works, eh? Rock on!