DS went through a similar stage for a month or so after DD arrived. it didn't start right away, proably from around 6 weeks or so... He also ran in and hit her once when she was sleeping. i was livid.
He has slowly learnt to not 'errupt' us when DD was sleepig. it's still hit and miss but getting beter. I sure hope things can settle down again for you soon.
It's always extra hard when they're sick, never mind if you're feeling awful too! Hope you're feeling ok