Hi Angela,
{{{HUGS}}} it's tough to get back on track after an illness.
I think that the first thing that needs to be addressed is the boob=sleep association. If she's only nursing for 2-3 mins then she just needs to suckle to soothe herself. Does she take a paci? This could be the best way to tackle this problem. and don't worry about it interrupting you BF relationship with her. At 13 weeks she's very unlikely to get nipple confusion

Also, unless instructed to by your doc you should keep on BF her. Just try not to breathe on her ( a hospital mask can help) and wash your hands very well before BF her. Your breastmilk will have anitbodies for her

As for her routine, keep things low key for a few days. She needs lots of time to rest and recover. Also, I think your wind down routine may be a bit too long for her age, so try to sing only one song and then do shh/pat to send her off to sleep.
Start the day at 7 or 8 (whichever you had before) even if she went to bed late at night. It's important for you to implement the routine since she's not capable at the moment. You will probably have a few rough days, but I'm sure you can get her back on track very soon!
If you need any help or support don't hesitate to give us a holler!
- Beca