It's going to be ok!!!! Be knd to yourself. Your hormones are going nuts and everything is probably feeling very out of control. Don't worry about a newborn. Not YET!
Is he eating well during the day again? Are night time bottles still necessary? If not, just go cold turkey back to what you were doing before he was sick. Pretend that this is always how you've done it. Give him medicine like ibuprofen or if that makes you nervous, tylenol at bedtime to be sure that he's not waking out of pain. If you know he's had enough food during the day, then sleep train him- my preferred method was a paci in place of a bottle when he wakes, but some don't like that. Pat shush or pick up putdown, or whatever you use that he knows. Personally, I think that if you wait until he's completely healthy, you may have a lot more work for yourself later. You need to remain consistent to a certain extent even when they're sick.