Trying to increasing print surface quality (E3D on Flashforge?)

[Dargonfly]

I have printed a lot in layer heights of 0.1[mm] and low speeds (25~50) and noticed that my prints had a 'wavy' pattern in the vertical direction.

This could have several causes:
- 'loose' X & Y belts; (tried tightening, still appeared on straight lines)
- mechanical jerking (tried changing acceleration settings and lowering print speeds overal - resulting in less waves at corners, but still present on straight lines)
- uneven filament (measured my filament at several places with my Mitutoyo, seemed to be good)
- uneven heating of filament (temps on Flashforge appear to be very constant, no real way of checking the output - could conduct a test with extruding at a MUCH higher temp than I usually use)
- damage / junk in nozzle (does not appear to be the case)
- nozzle size too large for amount of extruded filament (this could only be tested by using a smaller nozzle)
- general vibrations
- printing too fast for extruder steppers (not the case)
- printing too slow for extruder steppers (uneven extrusion due to low speed)
- feeding gear is damaged / too little teeth

This last one got me intrigued so I tried printing as usual but moving the bed way downwards (printing in the air) and noticed that the extrusion was a bit 'wavy' by itself: (thick - thin -thick - thin - thick - ...)

This is probably the issue I'm looking at, so that means it has to be one of these causes:
- uneven filament
- uneven heating of filament
- general vibrations
- printing too slow for extruder steppers
- feeding gear is damaged / too little teeth

As mentioned, I've already conducted some tests for the above, but will redo them a bit more serious now that I've narrowed down the cause (which hopefully is really is the cause!!)
Another thing to note here is that the wavy pattern on the final product (a cube for testing purposes) is very consistent with its location. This already rules out the 'uneven filament' because that would mean that it should be more 'random'. But since the extruder starts doing the same thing EVERY layer, it has to be one of the causes listed in bold above.
General vibrations I have already minimized as much as possible.. but this is more of the final cause if everything else fails (which means that that would be the limit of the surface quality.)

Uneven heating I will test by heating the filament MORE, why? Uneven heating could be a problem if different parts of the filament are in different 'phase' stages, if I heat everything way more then it should all be in the molten phase I'm looking for.

The 'printing too slow' is a bit more difficult to check, because yes; this doesn't happen at faster feed rates, but I want to be able to extrude with these layer thicknesses.
So I was thinking to get a bowden setup here, then running the motor 10 times as fast (in software), and using a gear (10:1) to allow the feed rate to be correct. This way any 'steps' of the stepper motor shouldn't be visible anymore.
Regarding that: has anyone thought about replacing the extruders with some E3D's? http://e3d-online.com/E3D-v6/Full-Kit
Does anybody know which voltage is used on the current extruder heating elements? 24V I guess? Would also allow me to print at 0.25[mm], or even better: use 0.25[mm] for shells and 0.8[mm] for infill with dual extrusion.

Regarding the feeding gear: this one works well. it 'might' create some 'step-feeding' of filament due to limited amount of teeth. But I do not want clogging of the extruder either due to a bad feed-gear.

Lots of text I know, but these were just some ideas, not perfectly organized either. I hope that somebody has some thoughts regarding this! If there is interest I will keep you guys updated with pictures of the tests I'm conducting (and the wavy pattern I'm talking about.)


EDIT: there's also general settings that influence this behavior like amount of shells, infill, layer height, etc. but for maximum quality and some durability of the model I often find myself printing at 0.1[mm] layer height, 0.4[mm] layer width with 2 shells and 15% infill - if the height-width rate isn't good, then switching to E3D would allow me to use a 0.25[mm] nozzle. Infill has almost no effect on surface quality with 2 shells. 2 shells looks different then 1 shell.

EDIT2: here is a topic that has pinned down the most (most topic disregard it as z wobble, which is not the case here) http://forums.reprap.org/read.php?1,214990
this picture shown (exaggerated) what I'm talking about:
(NOT MY PICTURE - MY RESULTS ARE A LOT LESS VISIBLE, BUT SIMILAR TOO THIS)