Underextrusion/skipping steps

Hello there.

I am having a problem that is really bugging me. I built a custom 3d printer for myself and have been printing with PLA and mostly ABS for over an year.

Recently I made some modification to my carriage (the major update was adding a part fan). After that I tried printing some PLA and had a serious bad time:
- the PLA would flow only at a really high temperature (over 240?C), even when the hotend is far from the bed;*
- lost a lot of material;
- experienced 4 clogs.
*below this temperature there is the clicking sound from the extruder motor skipping steps


Detailing a bit more...
After the first clog i did some cold pull clean up and was able to print the first from 4 models that I should be able to finish during the weekend (~10 hours printing);
The second clog happened during the next print, around 5-6 hours printing, this one was really bad (it clogged in the middle of the heatbreak);
The PTFE inside the heatbreak was partially burnt, not sure if was from previous prints or not;
I changed the nozzle (also seasoned it), heatbreak and heatsink. After that I was able to conclude the print of the second model (~14h);
When tried printing the third model I faced another clog around 6-7 hours printing, I did some cold pull clean up and tried printing again;
Experienced another really bad clog (in the middle of the heatbreak) and did not have enough spare parts or time to countinue struggling so I had to call off the job;
There was a green goo (not sure if it was from the PLA or from the vegetal oil that I was using as lubricant) that really stuck the filament inside the heatbreak.
*I was printing with 80 mm/s and 240?C, during long movements of the nozzle the extruder skipped steps at random. Below 240?C the rate wich the extruder missed steps were much higher.

After this incident I ordered a new pair of heatbreaks and swapped to the ABS spool that I was using before the modification. When I tried extruding ABS at 235?C (with the nozzle far from the bed) and the extruder would still lose steps, at a really high rate.

More random info:
Another modification that I did was updating Marlin from 1.1.5 to 1.1.9;
I believe that the hotend is an e3D v5 clone;
I use a fixed extruder with a bowden tube;
I printed a lot with this hotend last year, fisrt time having this kind of issue;
During the modification I noticed that the heater got a little loose, though that maybe the thermocouple is not reading the correct temperature BUT, if that was the case, it should read a temperature below the real one (since it might be loose);
I tried adding more current to the extruder motor while I was having trouble printing with PLA, helped a little but I am already at the limit (went from 0.6 V to ~0.65V) and it was working fine with 0.6V before the modification.

I will try measuring the temperature with a cheap infrared thermometer tomorrow. I hope that the only problem is a bad temperature reading, otherwise I don't know how to approch this anymore...

Anyone have any kind of advice/tip about this matter?