Dash lights inop with ignition on etc, '99' nissan almera gti n15?

Hi, wondering if anyone can help me with an on going problem with my almera gti. I have recently fitted a new 4 branch exhaust manifold and down pipe to the gti, also at the same time i removed my rocker cover for painting. After refitting the rocker cover and completing the exhaust replacement i noticed that i had no dash lights, interior lights, elec windows etc when switching the ignition on. I found that the car would start but dash lights etc still inop untill revving over 2000 rpm and everything would jump into life. I fitted a new starter motor due to the bearing causing excessive noise when starting and hoping being a shot in the dark that it would maybe cure the dash problem, no success. I checked all wires in wiring loom running across the rocker cover and found all ok (good continuity, no high resistance, no visual damage to wires etc). Also checked alternator charge voltage and found when started (with dash lights inop) alternator not charging, but when revved (with dash lights now working) alternator charging as normal. Problem has now developed further and now alternator will not charge and dash lights etc will not come on at all! My gut feeling is telling me the alternator is defective but i cannot understand how this would effect the dash lights etc. If anyone could help it would be much appreciated.