An idling riddle.

[Ghosts]

2001 ZD30, 5 speed manual, snorkel, with 243000 Kms and with no engine modifications. Recently, it started to have an idling issue, which it idles rough once I have driven around for some time and never happens when cold / warming up. On the odd occasion, it would skip a beat, but that has gone since the recent work I had done. I had rocker cover gasket, injector seals, injectors, glow plugs and the egr blank done recently. Those jobs made an improvement to the running of the vehicle, but the roughish idling is still there and goes away when the air con is turned on, but it only masks the problem I feel. The rough idling only happens when stopped with the motor running. On the testing machine that got plugged in to find faults, it showed the idling has decreased by 50 rpm and the injector pump has 46%, what ever it has, that makes it have 46%. I am wondering if any one has an idea? I have had the dual mass flywheel replaced 30000 Kms ago and the intercooler has a leak in it I`ve been told. Would a leaking intercooler cause rough idling, as a Nissan technician said it would, because it`s sucking in more air. I have found a few answers that may cause the situation I`m having, but like most problems, there are symptoms that are similar to each problem. I`m doing and thinking of the cheapest options first at the moment.
PS, MAF Sensor has been replaced with a new one.