If you are renewing your ME/IR SPA you will automatically get SE privileges and so no need for the IMC as your IR superceeds it. The only thing you cannot do is exercise those IR privileges on SE aircraft as your SEP has expired.
I would renew your ME/IR then apply for the licence, the examiner will sign your ratings page in the current licence. If you get a new licence first then you will have to reapply to the CAA to get the ME/IR put back in it as the certificate of revalidation will have been removed and the rating put on the back of the licence.
As for the SEP, if the ATO has An SEP course then yes they can do both however they will need to be separate as they are for separate ratings requiring separate tests. The MEP and ME/IR will be combined.