Thank you for your questions.
The two exhaust manifold gaskets were cracked and torn and in very sad shape when I removed the exhaust manifolds. I wouldn’t draw any conclusions from the colors other than it was due to bad exhaust manifold gaskets. The engine starts nicely, runs strong, and has good compression. I will find out how clean it runs in my 1984 XJ6 Vanden Plas when I get it running and I take it in for a smog check, hopefully before the end of January.
I considered leaving the intake manifold on until after I removed the engine from the car, but decided to remove it first for three reasons. Firstly, i wanted to reduce the lifting load before removing the engine and transmission together. Secondly, with the intake manifold in place the engine would tilt to that side making removal of the engine a little bit trickier (and it is already a challenge with all the hoses, wires etc). Thirdly, I was going to remove the intake manifold anyway and install the original one from my 1984 X6 Vanden Plas when I install the engine in that car because that intake manifold is still very nice looking from the restoration I did to it about 10 years ago. The intake manifold on my 1987 XJ6 parts car was in considerably worse shape with some rust and lots of greasy dirt.
Removing the intake manifold is a real PITA to be sure, especially some of the bottom nuts. But I was going to remove and replace it anyway, so I decided to remove it before I removed the engine. In this case the intake manifold separated very easily from the headso I was lucky there. I have had difficulty separating the intake manifolds from the heads before on other Series III XJ6 engines and had to resort to heavy pounding with a large mallet on a block of wood to tear the intake manifold gasket in the past. This one was very easy to separate from the head once I got all of the nuts removed.
BTW, I did remove the front bumper from the 1987 XJ6 parts car before I removed the engine and this made the lifting somewhat easier, but I still had to raise the engine/transmission pretty high because the transmission end hangs lower and I needed to get everything to clear the power steering rack and front subframe. I am still trying to decide whether or not to remove the front bumper from my 1984 XJ6 Vanden Plas when it is time to install this engine in it. I have some more time to think about that while I am working on the engine.