I would agree with your ATO that as your JAA licence has lapsed you do not have a licence. An FI is therefore required for your training. You are required to undertake a course of training for your SEPL as prescribed by the ATO HOT/CFI. This can go from zero hours to whatever is decided. Regarding RT, if you have held an RT licence in the past then there is nothing you need do for this other than complete the EASA licence application form correctly. Make sure you tick the request for the RT privileges box for it to be included in you new licence.
There is no such thing as an IR(R) but it is the only way the IMC rating can be entered onto the EASA licence. Until you renew the IMC(r) it will be entered on the back of the new licence in the lapsed rating section. (make sure this is done). Also make sure you tick the box for a national PPL licence. the IMC(r) will be included, using its proper name, on this licence.