Inconsistent printing results using same settings but different calibration models I've got a second-hand Renkforce RF1000 which I've gone into more detail about in this question.

The extruder works however, I get some inconsistent results. First I printed a calibration cube and noticed huge gaps in the bottom layer. Because of this, I increased the extrusion multiplier to 1.05. I noticed there still were some gaps but also other issues, I then printed one with the extrusion multiplier reset to 1.0 and a negative Z-offset. The results are shown below. In every image, the left cube has multiplier 1.0 and the right cube has multiplier 1.05.



Then, for a better idea about the consistency, I printed a hollow pyramid. This shows some heavy stringing. However, when printing a retraction test I barely get any stringing.







Does anyone know what could cause these inconsistent results? I assume some hardware tweaks might be needed, not just slicer settings. Any help is appreciated.


I use Slic3r
I use 3&nbsp;mm PLA printed at 190&nbsp;°C on a 60&nbsp;°C bed with some glue (doesn't stick without). The first layer is 200&nbsp;°C with a 65&nbsp;°C bed.
After three layers the fans are enabled. 
I have a negative Z-offset, it probably isn't calibrated 100&nbsp;% correctly
I don't know the nozzle size (a new one is being shipped) but use a size of 0.5&nbsp;mm in the slicer
retraction length 2&nbsp;mm &amp; 60&nbsp;mm/s
minimum travel after retraction 1&nbsp;mm


Print settings:


EDIT:
After the recommendations I've changed the following:


All belts have been recalibrated
The e-steps have been recalibrated through this method. Couldn't do a wall measurement due to a lack of precise tools. 
Changed first layer temperature to 210&nbsp;&deg;C and other layers to 205&nbsp;&deg;C
Added two top layers


I printed two new cubes. One without glue and with a Z-offset of 0.05&nbsp;mm and one with glue and with a Z-offset of 0.15&nbsp;mm. The results are quite comparable to the original ones although slightly better. Any recommendations? 

I'm aware of some cooling issues on my prints. Once a new nozzle arrives I plan on printing the current cooling system again. It's not really blowing air right effectively now.
First of all, I would try printing a little bit hotter, let's say arround 210&nbsp;&deg;C. Secondly, due to how the X and Y letters are being printed in the sides of the cube I would suggest to tigthen both the X and Y belts.

Regarding the gaps, I would first try a flow rate test. You could use a cube like this one.

Using: 


extrusion multiplier = 1
layer height: 0.2&nbsp;mm; 
layer width= 0.4&nbsp;mm ; 
wall count= 2. 


Then measure the walls with a caliper and you should have 0.8&nbsp;mm walls. Do a couple of measurements, get the average and divide  0.8 by it  and multiply by a 100 (100*0.8/average). That's your new flow rate.

I would also try to add 1 or 2 top layers to the print.

For the first layer, I would definitely get a glass bed and use hairspray. The bottom of the pyramid doesn't seem to be sticking well. Apart from this, I'm not really fan of using Z-offset. Just try leveling a couple of times manually with a paper to get it right.