I might give more pure alfalfa -- and *good* stuff, not all stems with the leaves long since fallen off and blown away as dust -- if I thought she needed more protein. All the other advice you've gotten is good, too.
Two other considerations:
First, I would bet you anything she still has a significant worm load, if she's only been wormed 2x since last fall. I would suggest at *least* taking some fresh poo to the vet to have them do a fecal -- and if the first time shows few worm eggs, do it again a couple weeks later. You might discuss worming regime with the vet as well... rescues sometimes benefit from an intensive 4-day series of wormers once their general health has been stabilized. I would also strongly suggest that the next time she is wormed, you use Zimectrin Gold (or equivelent) that gets tapeworms (which will not reliably show up on a fecal exam). Some people would use Quest, to get the population of worms in cyst form that are almost certainly continuing the problem despite your worming her -- but personally I would be real cautious using Quest in a run-down horse, and would at the very least want a vet's advice first. Anyhow, I think concentrating on worm eviction will make a BIG difference to her -- you would be amazed how much condition a heavy worm infestation can take out of a neglected horse (and a horse can remain heavily-infested despite several wormings, for a variety of reasons).
Second, has she been blanketed over the winter. If not, then just trying to keep herself warm (even in the barn) may have taken an awful lot of the calories you were putting into her. I would put a turnout sheet on her, still, anytime the temperature is below 50 degrees or so, until she is in better flesh. (Turnout sheet because they are generally more robustly built than stable sheets, and are more useful as well -- a turnout sheet will help you get her into turnout for a higher % of her time, which will really help her as well. It will help her gain weight -- yes, even though she'll be moving around more -- AND it will help get/keep her feet healthy.
In fact, if she has been almost entirely in a stall all winter, it is possible that some of the failure-to-put-on-muscle-mass that you're seeing is just lack of exercise. Horses that have *had* decent muscles in the past can put them back on to a decent degree just standing in the barn eating good food, but if she's been neglected for a long time or most of her life, that can be a different thing and she may need to be MOVING AROUND, not just for health and happiness but so that her body can construct some new muscle tissue.
(With the sheet, and turnout, and so forth, obviously you want to approach things intellgently so as not to scare her.)
Good luck,
Pat
