Robin, have you ever been on any other rollers? Maybe JKM have had theirs recalibrated since your first run way back when. I am aware that DD rollers are supposed to be the most tightly regulated, by the manufacturer - and if JKMs were being "over generous" when initially installed - a subsequent recalibration might have down-corrected their readings. I simply mention this because you seem to be saying that the stage 2 "seems better" - so your butt-dyno is telling you the stage 2 is better, but the RR is telling you the opposite.
Engine oil - what brand, type and spec oil do you use? And what is your oil consumption like? Do you religiously keep it topped up to the max by adding small amounts frequently, or do you let the oil get fairly low and then add quite a lot?
Onto the specifics of oil in the turbo discharge pipe. Firstly, you stated "Inlet seals removed and cleaned and all ok in that area now" - but do you mean the seals on the pipework, the seals on the turbine shaft, or do you mean the valve stem oil seals for the "poppet valves" in the cylinder head?
Regarding actually finding oil in the turbo discharge pipe, I think this is fairly common. I found oil in mine, and inside the standard intercooler - but it wasnt much. Maybe one or two tablespoons, which is fairly reasonable. However, I wonder if the stock GTI intercooler has something to do with this? I personally reckon the stock i/c is slightly restrictive, which can cause a slight backpressure on the inlet side of the turbo. Since upgrading mine to the S3 cooler and twintercooler, I do notice a much more rapid rise in turbo boost - which prooves that the airflow through the inlet tract is much freer and less restrictive. Maybe this is also having an effect on the way that the oil vapours from the crankcase ventilation system are not getting to the combustion chambers quick enough. Think of having a hot shower in a closed bathroom - the shower will steam away, but if you have a mega powerful extractor fan immediately above the shower head, it will suck out all the steam. However, if you have a clogged, weedy fan, the steam wont get sucked out, but will condense on your bathroom mirror, and then dribble off the bottom edge.
Onto a couple of other issues. Did JKM plug in a VAG-COM to check for fault codes? And did they carefully monitor the N75 cycle?
Regarding the actual replacement of the turbo - only you can decide which is the best way. However, I would personally never recommend any second hand turbo, no matter how well the previous owner claimed to have looked after it. You only need to recall some of the threads on the other GTI fourm (revving engines whilst stationary, "blipping" throttles, correct turbo cool down - I even think that you mis-understood about the cool-down procedure), and it simply showed a fundamental lack of knowledge on how to car for an engine in general, let alone the specific requirements of a turbo. If I were forced to only take a 2nd hand turbo, then I would send it to a specialist turbo re-builder for a complete overhall and warranty.
If your original turbo is knackered, I would personally seek a specialist recon, or go for the genuine new VW part. Yes, I understand your POV that the official VW 2 year warranty will probably be void - but it is the "peace of mind" from getting an OEM supplied part - you can pretty much expect an OEM new turbo to last a long while, but how long will a slightly cheaper second hand one last. The labour charges will be the same, but if the 2nd hand one doesn't last, then someone will be paying the labour charges all over again.
