Re: Fluke eggs - they only show up in FECs at certain stages of the life-cycle so you may miss them altogether in the faeces. Dose your ewes for fluke on a risk-based model, unless you know you have fluke (abbotoir kill data is a good way to obtain this). So, I would dose your ewes if the ground is wet. I normally have no fluke and have dosed a lot of mine, based on where they are/have been.
There is absolutely no point in vaccinating anything whos immune system is compromised as it will not produce the correct immune response, treat the disease with antibiotics, dose when the ewe is well.
(As a by-the-by, I expect this is the reason people are losing vaccinated sheep this year as opposed to the effectiveness or otherwise of the vaccine concerned, most sheep will have been pretty miserable this summer and could well have had low-level disease)