I don’t think Virgil’s character was at all well rounded. He was only the means by which Michonne was to find Rick’s discarded items. Never intended to be a character of any great importance. If things didn’t add up it could be explained by his losing his mind over his families death. He wasn’t supposed to be logical and seeing the way he acted it probably was for the best that he remained behind, alone on that island.

 

1) So Virgil promised his wife flowers everyday. Why did he leave the island then to go to Oceanside? He would have been gone for several days. Was he just looking for someone to help him clear the walkers?
When he locked up the people inside, he did not know his wife and kids were inside too. So, eventually they died (by hanging themselves). He admitted to Michonne that he was not good at killing walkers. He needed Michonne to go in and kill obstructing walkers and retrieve his dead wife and kids. His wife is the one that he put her shoes on.
When Virgil and Michonne first landed on the island, Virgil put flower on the grave which was supposed to be empty. Later on, supposedly after Michonne helped finding his wife, that grave actually had a body underneath.


2) If he needed someone to help clear the walkers why didn't he just get the other 3 people to help him?
He did not trust the 3 people.


3) How were his other prisoners getting fed while Virgil was in Oceanside?
Maybe he threw in some apples and other things enough for a few days?

4) How would he have gotten the food into Michonne's cell to drug her without her attacking him?
Not sure, was there an opening at the bottom of the door for sliding a food tray in?
Or, maybe, he just opened and shut the door quick enough just to slip some food in while she was sleeping?


5) It was hard to tell, but was that Virgil on the shore when Michonne was on the boat? So he stayed on the island to take flowers to his dead wife everyday (idiot if so). Wasn't sure if it was him or a walker.
Yes, it was him.

6) The map of the compound showed about 5 different Groups in different areas. It looked like the Michonne and the other 3 were in the Group 2 section. I was expecting that there'd be other people in the other Groups.

This is not clear in the show. Michonne did say she investigated every building. Could this mean the entire island or just her vicinity?

That island map showed 5 groups. I think there are names on each group. Could those names be building names or names of the people of each group. There are, maybe, at least 100 names in total.

Virgil said the 'others' came and brought violence and the sickness. Who are the 'others'? The 'others' cannot be one of the 5 groups originally there.
Also, that island is supposedly to be a navy research facility. It must be related to biological 'warfare' (?) because Michonne saw bones and remains of animals inside cages in one of the lab room.

And, I do not think the boat (with Rick's stuff) came to that island purely by chance. That 'boat' could be part of the navy and it actually went to the island (being a navy base) for a reason.