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are you using launcher pro? you can save your home screen there. as for apps+data titanium backup does that well. you can do a batch backup and restore. just make sure not to backup or restore system data. it will add system data from your previous rom and can cause your current rom to have major issues. as far as bookmarks go, i use dolphin and the bookmark to sd dolphin add-on app.
between the mikfroyo updates did you do a full wipe? becasue i do not think you would have to and thus may have saved everything think like that. unfortunately there is no single step or app that will do this. titanium just saves apps and there data.
you can actually back up and restore system data and pick bookmarks and other ones you want. just be careful because some system data are tied with the framework of the original rom and could cause problems. but i believe that was what you did previously. i have stayed away from system data because it caused a boot loop on my phone awhile ago. i only backup and restore apps+data.