Hi. I am also the same in that I started back my fluoxetine on Thursday so today will be day 3.
I take it in the morning now. The first time I used it I took it before bed - simply because I'd previously been tried on Citalopram and it made me feel absolutely horrendous. I'd take it then feel horribly sick and completely wiped out all day. I know these side effects are common for many people for the first couple of weeks but for me they just didn't wear off at all after time.
I've never really had any major side effects with the fluoxetine fortunately.
At one point I wondered if taking them before bed was affecting my quality of sleep (as if it wasn't bad enough already).
So the second time I was on a course I changed to taking them in the morning. This was mostly because I was working nights at the time so that was bedtime for me. I then started switching times about depending on whether I was on shift or not.
So basically if I was on a day off or on dayshift I'd take them in the morning and if I was on a nightshift I'd take them before I went out to work.
The half life of fluoxetine is pretty huge, measured in days rather than hours. It can be from 1 to 3 days at first and then up to 6 days after using for a period of time. So in that respect it's not absolutely crucial that you take it at the same time every day if you were to forget for example. To be fair, once you have established yourself on it, it really wouldn't make any difference if you accidentally forgot to take it one day and just took it the next day.
Just don't do what I did and forget or not bother more than you actually take it, then before you know where you are you've taken yourself off it!
Please keep us updated and let us know how things are going with this. I hope the side effects you are feeling wear off and pass soon.