Does Ubiquity respect my former partition layout with a new installation?
In my experience, upgrading or replacing my previous Ubuntu installation disregarded my previous partitioning method and built it's own (using ext4 of course).
I would go on the custom partition step, then select the partitions one by one (the size of the partitions are the same as the old installation), assign a filesystem, and check 'format' on each of them except swap space (if you have it). And remember to assign the correct device for boot-loader installation!
Hope this helps.