2006 Honda Civic long cold start, lights flicker

Hi guys,

I wonder if someone can help me with an issue in my 2006 Honda Civic EX.

I have recently been experiencing a longer than normal crank before the engine turns over, when the engine is cold. For instance when I first start the car in the morning it takes perhaps a 2-4 secs of longer crank than when the engine is warmed up. The same thing happens when I start the car after getting off work.
Secondly my interior lights and the headlights flicker sometimes. This issue had been there for a while, I changed my headlights to HIDs as a temporary fix and it worked fine for about a year. But now out of blue these HIDs start to flicker like flashing them on and off. I have also unhooked the battery while the car is idling and see that all the lights flicker, which I am not sure is normal or perhaps there is an issue with my electricals.
I have checked and cleaned/re-tightened my battery terminals but it did not help.

I have gotten the alternator inspected by the autopart store and the test came out to be ok.

I am suspecting it to some either a relay issue, an alternator voltage regulator, or some grounding issue.

I am wondering if anyone can guide me in the right direction to nail down the issue?