P0300/P0303 code, flashing check engine light, bad idle

So the car is a 2004 Dacia Logan 1.4 MPI with aftermarket GPL installed since a couple years, owned by my family since new, currently owned by my brother, with 105.000 km.
The car has a check engine light since December, it only appeared after the battery drained while I was cleaning the interior, after I wanted to go for a drive it didn’t start, it was left sitting for a week before we jumpstarted it, left it running for a time, got for a drive ,engine was good, battery had good voltage (12.6 while resting). The CEL was throwed first in December, since then the idle is rough, around 600 rpm instead of around 800. The car used to stutter but now it’s gone after following replacements/repairs:
-Everything related to ignition: Spark plugs, Ignition coils, Coil pack
-Valve adjustments was done by a service
-Recently changed oil/filter
-Cleaned throttle body/ replaced Air filter
The P0300/P0303 code indicates a misfire at the 3rd cylinder which could be true due to the rough idle but we can’t find the cause. Only the injectors and compression weren’t tested. Maybe those are at fault.
Another info is that the car runs on GPL most of the time, rarely on gas. Tomorrow it goes to a revision for the GPL system.
The head gasket should be good, there are no leaks, the oil wasn’t creamy. No oil leaks. No blue, white or black smoke. The car was always warmed up during it’s lifetime without abuse regularly maintained. Distribution will be changed soon (Cambelt, water pump). Any ideas what could be causing the issue?