Engine questions and discussion

I have recently acquired an m54b25 short block pictured below. My plan is to take it apart and learn as much about the M54 engine as I can. Then rebuild it with a slight upgrade in performance but mainly reliability.(Im not good enough on the track to need a monster). I have read the threads by PEI330 and jimmyobergs, both a wealth of information but still have some questions and wanted to use this thread as a way to discuss things throughout the process. This is my first time ever inside and engine but I am mechanically inclined.

So far I have completely drained it and removes the majority of the accessories that it cam with. I am currently stuck on how to get the Harmonic dampener off so i can remove the front cain plate.

Also i have a few questions about the engine.

1.How the hell do you guys get it so clean? i tried a piece of the OFH by hand and it was still not that clean and as you can see this is a dirty block.
2.The circled items in the red the one on the top is a dowel correct? and they should just pull out?
-The second is a stud on the side of the engine for what im not sure but whats the best way to remove it? when i rebuild i will use all new hardware?
-Third is a mangled blue plastic piece which real oem called a some sort of transmission plug. I have a manual so whats it for and what should i do with it?

Thank you for any help
James

The second circled item (i.e. the one in the middle) could be a couple of things. It could be a stud that the under-manifold harness casing bolts to or one that the dipstick bolts to. I'm not certain, but it's likely one of those two things. Open up your Bentley and have a browse... or, if you're really adventurous, remove the intake manifold on your E46 and have a peek.

This should be a really interesting thread. Good luck!