Please Help!

I rescued a rat from the street about a month ago. When my fiance was walking our dog he noticed a rat and sent me photos of her and right away I noticed she was not your typical street rat she appeared to be a fancy dumbo. I wizzed over immediately and scooped her up, she was in bad shape. Immediately I ran to the store to get some make shift bedding and supplies to tide her over until I got a better set up and surprise, surprise, she went into labor! Sadly she was so wiped and on short notice I was ill equipped and so the babies passed shortly that evening. Since I have upgraded her to a huge cage and hooked her up with all the fixing and got her in tip shape and medicated. Although I am battling her sneezes and nasal discharge. Initially I had paper bedding and she continued to sneeze so I changed to aspen after 2 weeks. Since the switch she seems to be having even more red nasal discharge and sneezing. No discharge from her eyes at all and she is on Doxy 2x a day from the Vet which has helped her breathing. She has also cleaned up super well and is all healthy and pink again. Her behavior is fine she jumps, plays, eats and is starting to trust me when im around with treats and such. Given my research she appears to be around 6-8 months old. She is my first rat and given her traumatic past I just want to give her the best life possible but im completely out of sorts at what bedding to use and the internet hasn't been much help. It seems no matter what I do I cannot rid the beddings of dust and she just keeps sneezing. I just bought a fleece liner to try and use in the interim to try and let her airways heal a bit. Im pretty vigilant with cleaning so increased maintenance isnt an issue with me. Any advice would be super helpful! (Also aware she will need a friend so im on a waitlist with a local breeder and rescue group- In Portland)