yes, Thomas was right. You must remmeber this. Your result was only by tuning A/F only but not ignition timing. As i said before, power comes frm ignition timing but not A/F. A/F only give u smoothness. So 3whp and 3wtq to me is healthy.
Another thing is your fren gain was based on auto. Auto ecu setting could be diff or by stock, more on safe mapping. Hence after Emanage tuned, much gain was able to be realise. Unless you do have same manual Neo, abt the same mod, tune with emanage and gain 15whp then yes, i do agree with your dissapointment otherwise its not apple to apple comparison.
As for gear ratio wise, hm..... ok, diff tuner diff way of doing. Some will use 2nd on auto to tune, some will use 3rd on auto to tune. Same goes for manual. Its either 3rd or 4th. Reason why they use higher gear (4th) is they wan more load and also for more accuracy A/F tuning. If the gear ratio too short, its hard to tune and capture. On longer gear ratio, you can tune and capture the A/F more accurately. Of course for shorter gear ratio, you will see higher hp gain.
But 1 thing im not sure is why they use 4th gear on your engine. Coz normally on lower engine capability output (not turbo) they will use 3rd gear to tune. But then maybe your 3rd gear ratio may not be suits for tuning. im not sure. Also, bear in mind, your GB ratio wasnt the same as the stock manual Neo ratio. Who knows, your result could be damper by your "new" gear ratio and might fetch higher value on stock ratio.
Also, as i mentioned to you earlier. your could run lean and seems like i was right. With all your mod to improve your exhast and intake, your left out the fuel. With your exhaust gas now able to dispelle faster and more efficient, more air intake is possible now. With more fresh air intake = more O2. more O2 but less fuel = lean. As i explained to some bros on last TT about cam overlapping, with your exhaust gas able to dispelle efficiently, a small vacumn effect will generate in the combustion chamber that will suck in more fresh air from intake valve open.
So with all your intake and exhaust mod, im not suprise you run lean. There is this much on how much stock ecu can compensate on fueling so never expect or think the stock ecu will able to compensate which alot of plp do. As your injector will only max inject X amount of fuel, with so mcuh more air going in, you do run lean. As for cause some wear and tear to the valve seals or somehting like that, posibility is there but im doubt chances of it will happen.
Perhaps he detected some serious amoutn of knocking, hence he suggest you do a compression check. What is your before A/F ratio?