ATPL exams and CPL flying course are two sides of the same coin, hence you need to do both under the same jurisdiction unless the ATPL exams are specifically recognised by the Authority which will issue your licence. Ireland and UK have recently agreed to a reciprocal agreement to recognise each others exam results.
An IR is a Rating, therefore can be undertaken in any JAA state, and is seperate to your licence wrt country of issue.
Can't help with the ME issue I'm afraid.