Configuring Marlin and print starting too high

I am having some trouble configuring Marlin..at least that's what I think the problem is. It's a P3Steel built from a kit with leadscrews on the Z axis.

Imgur Album

I tried configuring Marlin following this guide and Prusa's Calculator. I'm not sure however that I entered the right values.
My stepper motors have 200 motor steps per rev.I am using DRV8825 drivers so I assume I am using 1/32 microstepping. I am using GT2 belt (2mm) and 20 teeth pulleys. After also measuring filament I for E steps..this was my line in the config.

#define DEFAULT_AXIS_STEPS_PER_UNIT   {160, 160, 3200, 200.9419152276296}

The problem I am having is that when I start the print, the nozzle is too high from the bed but when I auto-home the height is correct. I also followed the manual leveling process. This is the file I am trying to print.

I am using Slic3r and Printrun. In the imgur link you can find my Slic3r settings. Please, help me, it's driving me crazy because I haven't been able to get a single print out of my printer

Edited 1 time(s). Last edit at 09/04/2016 04:34PM by bitemyshinymetal.

With Slic3r, default setting is to home all axis and start heating the bed.
After bed is warm, it will lift Z axis (nozzle) about 5mm and starts to heat nozzle. (G1 Z5 F5000) (So you can use tweezer to remove that goo that is oozing out from the hot nozzle)

When nozzle is ready and warm, it will come down to the first layer, which looks like you have set to 0.4
This is why the Slic3r wants 200% extrusion for the first layer, because the real distance between the bed and nozzle is not 0.4, but 0.4 + (distance between bed and nozzle when home)
The real distance might even be 0.6, but thats why you compensate by extruding the first layer 200%.

Edited 1 time(s). Last edit at 09/05/2016 07:08PM by Veesta.