Misfire code, rough idle, full tune up complete, crank sensor replaced, intake replaced, injector test good, exhaust clear no codes other than misfire, trim lean once

The black soot on the plugs means that you are running extremely rich. The fuel injectors ma test good electricly, but they are notorious for leaks. The spider-looking thing sandwiched between the plastic intake plenum and the intake manifold gets cracks in it's "legs" and leaks fuel ito the plenum area. The fuel pressure regulator is also housed in this same assembly. if the diaphram in the regulator gets a pinhole in it, it also leaks fuel into the plenum area, causing all kinds of erratic idleing, black smoke from the exhaust, and will cause your fuel trims to drop into the negative 20s.

There is a technical service bulletin covering this subject. This procedure outlines the steps required to replace the existing Central SFI Fuel System with a new MFI (Multiport Flexible Injection) Fuel System.

It is removing the injectors which are all housed in the center body of the injector assembly and replacing them with a new version where the injectors are located where the ols "poppets" used to be in the intake manifold ports. The picture below is for a V-8 engine that is covered by the same TSB.
The poppets and the pressure regulator are available individually to fix your existing fuel injection system, but I gave up on that after replacing several poppets only to have them come back in a few months with another popet line broken. I recommend replacing the whole assembly with the new and improved version. My customers have told me after doing this that the engine never ran that smooth when it was new.

The GM part number for the new injector assembly for your V-6 engine is 12568332 it is also now available at several aftermarket parts outlets.

As for the timing chain solution posted by doodieman200, all I have to say is that I have enough fingers on one hand to count all of the failed timing chains I have replaced on these engines. If you don't have a cam/crank sync code, the timing chain has definitely not slipped a tooth.

Reman 06 8.1 GM mis fire 4 and 7 , has spark and fuel
?? tone wheel teeth

Hey there im assuming this is the 4.3 vortec if you've done a complete tune up and have to check engine light id be looking at timing. An i dont mean distributer i mean timing chain the 4.3's are knowin well for timing chains stretching and even sometimes skipping teeth. That will give you a rough idle and a miss fire. Id give that a try get a shop to put a timing light on it and see if its out of time ive had this problem before and that fixed it