I just upgraded from OSX 10.6.8 to Yosemite. No problems except that all of my custom Mail stationery was missing. Bummer.
Good news - it was easy to fix. Here's how to do it.
1. Look in your backup (Time Machine, Carbon Copy Cloner, etc. - you do have a backup don't you?) and follow this path:
~ / users / (your user name) / Library / Application Support / Mail / Stationery / Apple / Contents / Resources / Custom
2. Copy (command c) the Custom folder
3. Look in your new Yosemite HD and follow this path:
~ / Library / Application Support / Apple / Mail/Stationery / Apple / Contents / Resources
4.Open the Resources folder and paste (command v) the Custom folder that you copied earlier.
Worked perfectly for me. Hope this helps!
BTW, if you have problems scrolling through your custom stationery, try going into your System Preferences>General and choose Show Scroll Bars>Always. There should be a scroll bar below your stationery.