UPDATE:

Hey all, just wanted to close the loop. I've been away for a few weeks but finally managed to install the injectors and put the 35D back together. It finally runs and drives! THE FINAL SOLUTION TO THE ROUGH IDLE WAS A NEW INJECTOR. So here's a quick recap if anybody ever has a similar issue.

I cleaned the injector bores, installed new injectors and all fuel lines. During the time that the car sat disassembled, I cleaned the intake manifold assembly (by soaking all the parts in Purple Power). After soaking for 2 days, the manifold, swirl flaps, etc, all came out carbon free, I just needed to wash it all off with water and dry it. Once the manifold and all the miscellaneous items were installed, I bled the fuel lines via the Foxwell scanner. Coded the injectors (kept 4 in the same place, but switched #1 (new Bosch) and #3(old #1 Bosch injector). After a couple of cranks, the 35D started right up, no more shaking and rough idle!!

After warming up the engine, I took it for a test drive around the neighborhood. Right away it was smoking heavily, a bluish cloud was blowing out of the tailpipes any time I accelerated. It seems that a lot of oil was accumulated in #1 cylinder and since there was finally combustion in that cylinder, all the oil was being burned off. After about 5 minutes, the smoke dissipated and the 35D ran fine.

After a couple more start cycles I did get a few more codes, one for a failed #1 cylinder glow plug, another for passive tank low circuit. Time to take off the manifold again.. The glow plug came out with a missing carbon tip, I tried to vacuum out the broken tip with thin straw via the glow plug hole, but it didn't work. I'm not sure if that tip is now somewhere in the DPF filter or still in the cylinder.. Anyways, I installed a new glow plug, re-installed the manifold, added a bunch of DEF fluid to both passive and active tanks and started driving the car. After almost 400 miles, the 35D is code free and runs like a champ.

Just passed the smog here in CA last week (with 2 monitors not ready), and finally registered the car in my name. I'm still not completely sure why #1 cylinder injector failed but it was the only injector that was covered with oil, so I'm guessing the oil plugged up the injector and it failed over time. I'm not sure if this was the culprit, but I did have a cracked CCV hose that I also replaced during the down time. Hopefully the fixes should give the 35D a lot more time on the road.

Just wanted to say a big THANKS for the input and words of wisdom to all that contributed to this thread. Could not have fixed it without you all!