Interesting question. I love finding alternative solutions from on-hand materials!
You're on exactly the right track with layering. This isn't what you're looking for, but I mix and match layers of Polartec outdoor garments to vary my thermal protection as needed.
Sounds like you don't have many of those kind of garments on hand, so the next best thing will be to use your thin fleece garments for a wicking layer next to the skin, then build loft with bulkier fabrics, such as coarse-knit wool or synthetic fiber sweaters. Such sweaters can be picked up at rummage shops for next to nothing, if you don't have a box full of them already.
Try to avoid constricting circulation or restricting range of movement with excess material, especially at the armpits or knees. Consider cutting the arms off a cheap sweater to build up the torso area and not jam the arms.
A chest pad of synthetic material can greatly reduce heat loss in that area.
Finding something for the legs will be a little harder, but you might find your flannel works, provided it isn't cotton.
Try to avoid cotton, of course, because it will get damp and cold.
Here's some more details on how I use layering.
http://www.scubaboard.com/showpost.php?p=2603629&postcount=12
HTH.
Dave C