Highest damage in a single shot

I think I  played in a very similar way to you. I also prefer to do side quests before going deep into the main story (because we're both sensible and don't rush ), so here's what I've done so far:

- Did as much of Eos as I could, right up to activating the vault using the basic rank one Avenger assault rifle, pistol, and whatever sniper rifle I could get hold of.
My first custom weapon was the Incisor sniper rifle, but it turned out to be far inferior to it's ME:2 and ME:3 counterparts, pathetic damage, and lousy recoil. That was a bad move, and a waste of research points.

- When I'd gone as far into Eos as I could at that stage, and while I was waiting for the rest of the radiation to decrease, I moved on to Voeld, still using the rank one Avenger rifle, the crappy pistol, Incisor and whatever armor I could scrounge from dead Kett. I was doing rubbish damage with the rifle, but it was enough to get me through, and it also taught me to fight smart, and strategically - in many ways it did me a favour.

I kept on with this setup until the main quest on Voeld, during which I got a new rifle from another dead Kett that was a big upgrade. I persevered with this until I'd activated the vault, after which I was able to get the science AVP perk that gave me free Milky Way research data.

- Crafted the rank 1 Revenant, and returned to Eos - by this time the remaining radiation had dissipated. Did most of the remaining side quests.
The Revenant is certainly not the highest damage rifle in the game, there are far more powerful assault rifles, but it's certainly one of the most efficient weapons. It's huge clip size, and high firing rate, means that you can just keep fighting on and on with it and rarely run out of ammo, and it's excellent for suppressing fire. My philosophy is that a rifle without bullets (or technically heat sinks) does no damage, and I'd rather have something slightly less powerful that keeps me in the fight longer than some novelty rifle that does huge burst damage for a few seconds, then runs out of ammo. The Revenant still does very decent damage - it's just not the highest.

- Went back to Voeld, kept on upgrading with my new incoming research data, improving the Revenant, and also crafting the Black Widow, and N7 Armor. Did the remaining quests, and also spent a lot of time mining. I followed each new rank of weapon I made with disassembling the old one to get some materials back.
My final act on Voeld (at that stage) was to drive to every mining node, and mine each one dry. I now had plenty of minerals for more weapons.

- Next went to Havari. Kept on periodically returning to the Tempest and upgrading my weapons until I got to rank 4.
Completed  Havari, and got final AVP science perks that cause research data to come in much faster, and more of it. Now I can make pretty-much whatever I like (level appropriate) and never have to worry about research data, or materials.

If you want Remnant of Andromeda research points, the best way I've found is to scan all alien tech you encounter, and also do the 'strike team' missions.

Hope this helps you a bit