Try watching the train derail at a very low speed to see exactly what is happening. Anytime my EN derails, the position of the cord connecting the engine and the tender is the culprit. Make sure you have enough slack and it isn't twisted.
I ordered from Amazon after Lego cancelled my order, too. I'm not happy with SAH, but the rep on the phone said there was no way to get me an Imperial Flagship.
I have that problem when the PF cable doesn't have enough slack or gets caught on a minifig in the cab. Make sure the cable isn't twisted or stuck on anything. Also try going over the problem area at very low speed and watching exactly what's happening.
The newest issue of Railbricks (number 9) has an article on building pantograph wiring, which is called catenary. I'm just reading it now, but it looks pretty good. It even has some instructions.
You should call customer service anyway for a new sticker sheet, but you may just want to move the odd dishes to the feet. It sounds like they changed the mold, and you got a mix of old and new parts.
I've never done this myself, but I would base the scale on your doors or windows. Is there any part of your house that will be hard to reproduce or call for a specific part? Let that determine the proper scale.
I actually got a free copy of Lego Universe with my latest catalog because I am a VIP member. I don't think I've ever gotten any mail I didn't want, but it's possible.