More Awesome Than You!

My legacy family has gone AWOL after several in game borkings and general fuckery. I have a feeling that this is because I reinstalled The Game on a new disk and just copied and replaced the old Program and My Docs EA files where the new ones were, the old folders having all the store content, patched from reloaded to razor and then with the official Patch. I reinstalled AwesomeMod and Indie Stone (sans core) separately. Just then when I was trying to save the game closed completely and came back with the Ramirez family whom I have never played or even heard of.

I've more or less resigned myself to the fact my legacy family is gone, but what I would like to know is what are the bare minimum files to transfer my old neighbourhood, households in said neighbourhood (if it's a different file) and settings? I can always just reinstall my CC and repatch the game, but I'd like to give saving my Sims one last go. I know there is probably a veritable assload of files I have to transfer, but any help would be very much appreciated.

Are you sure your current household wasn't just switched to another house? If it moved them to another lot while story progression was on?
Your family might still be there but the thumbnail might not be loading them (you'll see a ? cut out family icon).

Are you playing a Riverview save? I had a problem with it on reinstall, because my I did not reinstall Riverview and other store items first before loading.

No, I never play other households, the neighbourhood they were in isn't there at all.
When I came back it was Ramirez with the family cut out but I couldn't play them either. Also they were in Sunset Valley, I was playing them and hadn't re- or un-installed anything since saving them, but I think perhaps the initial way I installed the game and transferred files caused their inevitable demise.

I am aware that double posting is not allowed and I apologise for any toes that may get stepped on, but I figured that waiting two days and then reviving the thread would be better than making a new one.
Perhaps I was asking too much in my original post. I've made a new game and if anyone has an answer to my original question I'd be very grateful to hear it. However I understand that this may be asking too much, so instead I would just like to know this;

Where are the customisations and re-colourings of objects saved and is it possible to move them to a new game? I know it's anal but I'd like to be able to re-introduce my customisations if it's possible.

Try starting a new game in the same town as the old family.  Once you are in the game, go to edit town.  You may see your legacy family in the household bin.  That happened to me once early on, and the family was in the bin, however, they had lost everything previously associated with them.  It just might help you to save your actual Sims, though.