Poor puppy!!
I'd go back on the chicken and rice, first, and I would also get her a good full spectrum probiotic - quick.
All the antibiotics have probably depleted her gut-bugs, and those can take a while to build back up without extra supplements.... giving bad bugs a chance to get a toe-hold in the system.
We use a supplement called "GI Support" from onlynaturalpet-dot-com that has probiotics and also some herbs that support the GI tract and mucus membranes. It helps Denna when she gets an 'upset' for any reason.
We also have a tub of "probiotic miracle" on hand for occasional supplementation. It has a pretty good variety of probiotic strains in it. But, your local pet shop should have some good options, too. If you have some plain live yogurt in the house, and you don't know of a milk sensitivity, you can give her a dollop of that with each meal until you can get a better dog-based formula.
Does the kibble have chicken in it? Some dogs (a lot of mastiffs) are sensitive to the processed chicken in kibble (even if "real" chicken is ok - i.e. the stuff you're cooking with the rice).
My sister's dog had to go on a hypo-allergenic food to get her sensitive gut in line... she suffered from stress-induced-diarrhea, so anytime we got together was a problem (i.e. holidays). She's a high-anxiety border collie/heeler mix, though.
Hope you can get her back on track!
With her being a bit on the lean side, I'd opt to give her extra food for a while, maybe not "to appetite"... but a few big meals might not be a bad idea... except... too much food can lead to runny poops in an otherwise healthy puppy... and if her system isn't properly digesting what she's eating now, adding MORE food isn't going to help matters.
As for "how much" is the right amount to feed... Our vet suggested putting down a big pile of food, and giving the puppy 20 minutes to eat... they should leave some behind. Note how much was consumed, and use that as your starting point for portion sizes... after that, you go by body condition and adjust as needed.
Oh, and another thing you might consider getting once you're back online with normal poops and off antibiotics... is a cranberry based supplement to support the urinary tract. We had good luck with cranberry supplements with our cat - she had one UTI, and we NEVER wanted to repeat that experience again! We have a product called "cranberry wellness" on hand, too (also from onlynaturalpet)....
Good luck! Let us know how it goes.