Maybe it is a lot easier to fit a JDD gearbox (Dif Ratio = 3.157, 5th = 0.658) and swap fifth gear from 0.658 to 0.625. this gearbox was standard in the seat ibiza ecomotive with the 1.4 PD TDI 80cv (polo BM, etc) and the proposed fifth gear that uses the same spring plate is also from a SEAT Ecomotive (but Leon, Altea, etc and recent Bm, Greenlines, Ecomotives, etc.).
The serial numbers are:
02Z 311 361 B
02A 311 158 AQ
Also yo can fit 0.622 and 0.588 5th gears that are very close to mad taller gearing on FJW/FSM i'm not sure but i think that D.R(V-VI)=2.407, VIth=0.756)
JDD is a kind of JXY gearbox (D.R = 3.157, 5th = 0.700) but with taller 3rd to 5th gear.
I think It will be easier to find parts from (unknown ¿ecoboring?) cars produced in the 2008-2010 and nowadays, than a 6v from 2001 to 2004 (FJW, FSM) that much people wants to pimp their rides when they add lots of BHP to their TDI of the most sold VAG platform because VAG mounts short 6v gearboxes from 2004 to now, losing lots of top speed.
It seems that the longest gear ratios will match exactly the ECO torque curve at 100 kph, but i think that the load of your engine now it is not so diferent. But i d'on't think that the lose of your engine tranny between 1800 to 1600 rpm will reduce fuel consumption a 0.33L/100km (you will need a freewhell and a downhill slope to maintain speed and saving almost the idle fuel consumptiom of you engine). maybe non linearities of the BSFC versus engine load will help also and improve efficiency with taller gearing, but i think you are very close with your actual gear or tires.
You said that your 5th actual gear has a freewheels on it. Will the manual gearbox add engine drag fuel consumption?
I think you will need to change you engine and downsize it to a smart 0.9 cdi to lower the fuel consumption at low speeds. or lower your cd more. or maybe chopping a cilynder
You have reduced several L/100kms the fuel consumption at top speed, i'm sure. but 100 kmhs seems low speed in a very light, aerodynamic, low rolling, good power to weight car. Good lock on finding the right gearing to save the needed fuel.