having a remap wont effect EML warnings unless with in the mods the self check eml file for that controller has been pulled off ecu,, ie on say a egr or cat some of the files when these are removed ie i have decat on mine so the map was wrote to convince the upstream and down stream 02 sensors there is a slight difference in the signal voltages so ecu thinks the cat is still there ie if cat was there still there would be a difference in signal voltages,, when when t removed they will read same voltages,
as for remapping a broken car before fixing the broken part is a hard one not something i would do run all kinds of risks with hurting it for a start,, also will like you are now in nowhere land with knowing whats going on,, is it possible to reload the standard map then code read it again see what it flags up would be what we would do,,,
that said just because a car has been mapped or mods its normally possible to worl out whats doing what by a live data run or two but like said before need a good scanner,,
as for your approach of as anyone else had same issues and what could it be,,, so many things on them that will give same outcomes,, so needs to be scanned correctly and a number of tests done,, ie smoke test the boost side of pipework, smoke test the vac side of it,,, one thing very common on n14 engines is under the inlet manifold right at bottom of the engine block there is a vac expansion tank it had two small vac pipes going to it it also has a recess that collects any oil leaked from pcv or vanos valve at rear of engine this over time makes the rubber go soft this dumps the vac thats needed for the waste gate on turbo...failing this then put a vac gauge on the turbo wastegate check that it gets to max travels at 14psi on bump stop and stays there ie no leaks, failing that map sensor ie n14 has two one on inlet manifold and one on pipe at top, with diagnostics ca see what boost is actual and prescribed figures, ,