"I'm confused by Section 6.D instrument Flying."
Try 5D on SRG1161
"The left hand column asks for total hrs but doesn't give any space for insrument flying other than with an instructor."
"I have IF time from my FAA IR so my total IF time is more than the sum of instructional time."
Its not relevant to getting a JAA IR
"Also, since the IRT itself was conducted under (simulated) IMC there's no opportunity to claim those hours either."
As you have to meet the hours requirement before you take the test, thats not relevant either.