Two New Glow Plugs, New Symptoms

[Tpawlik]

I replaced the first four glow plugs before winter. I could not get to the last two. The car started well all winter with the temps in the teens. Recently it was starting poorly, running rough and lots of unburned fuel smell until it warmed a little. So, I pulled the intake manifold and the last three injector lines for access to the last two glow plugs. Now it starts right up but misses a little and is nailing. I have cracked the injector lines several times to get the air out. There are no air bubbles in the feed line to the secondary filter. The filter has about 10k miles on it. It is still not as quiet at idle as it was before I changed the last two glow plugs. Before it was really quiet.
What's the deal?