Hey mof, I tried to detail my Space Shuttle playfield swap as best as possible on http://abpinball.com, maybe that can be of some help - ping me if you have questions about anything I posted.
Re: order - I unscrewed everything on the old one bit by bit, and on the new one did the things first that would otherwise be a pain with the wiring harness in place - the tee nuts and solenoid brackets mainly. The dimples were way off on mine and for the most part I ignored them - just place them where they need to be to function correctly. I also transferred the wire holders very early on as I couldn't see a good reason not to, and it would have been a pain to catalogue them all otherwise.
As for what's the hardest thing, not really anything actually - it's more a challenge in scale... It's a large number of easy tasks that when put together amount to a really big one The one task I was most unsure about was probably the pop bumper bracket screws that need to be flush on the top side, but they turned out great too and it wasn't really hard in the end - see this post: http://abpinball.com/2014/02/23/installed-pop-bumper-bracket-screws-on-space-shuttle-pinball/
regards,
Andre