Yeah its a bit of time to get used to the new mod system. The added hipfire as opposed to sighted fire means how you mod your weapon can have a big impact on what you want to set your gun up for.
I am not on the game right now but basic over look is this. When you shoot that weapon do you use the scope or are you more often squeezing off fast shots and not useing the sights?
The other mods will say if they add or subtract by saying such as "Improved hipfire" "inferior" "superior".. etc.. Its hard to always tell whats the best but I just go Superior means the beter then say excellent, and excellent is better then say improved.
If you most often use the sights you want range and accuracy up. When you use weapon bench you will see what the mods add to or subtract. The scopes that sight in best are not meant for close combat and suffer accuracy when fired "from the hip" You may want to swap to something more of a compromise. This is why I set myself up with a weapons set that covers all the ground but with one gun for each main situation.
Anyhow you can set weapons up that work against each other mod and basicaly have a piece of junk made out of what could be a decent weapon. Like its handled for hipfire but ported and having a longrange scope and a mounted bayonette.
All I can say is take time and read the mods. Pick weapon mods to suit your Long range, Mid range, short range situations. Which means yeah you need to pack more then one gun.
With distance weapons you have to get used to the sway or hold your breath.. Unless you are in VATS and even then keep in mind if they are walking on a railed catwalk for example you may very well hit a railing even if its saying 96%
most of the time i hit stuff a lot better, am more aware of my surroundings and have more ap when using reflex mods instead of scopes
Reference to a unique weapon:
... I use that same weapon for both scoped fire and hip fire. The way I modded it is with a short barrel which technically halved it's range, but kept all of it's hip fire accuracy. I also gave it only a medium scope, as that is easily sufficient magnification for me to aim properly. Despite it's shorter range than what I could get with a long barrel, I rarely encounter an enemy that is so far away I cannot hit it. For those very rare instances, I keep a six crank laser musket on me. For fast moving close encounters like bugs and ghouls, I keep a short barreled shotgun, tricked out for short range of course.
My experience may be colored oddly however because I never use VATS, ever. All my gun fire is FPS. For that, it is quite possible to have one weapon that does the job 98% of the time.
Well not using VATS ever changes things up a good bit. Finding such a balance as you did in your main weapon is something that takes some time and thought. Or experimentation. Even so sounds like you favor 3 weapons. Also every gun can be used as a melee weapon. So it sorta doubles our usage.
I carry a few, and even throw in a weapon that also double functions as some other weapon but is energy based, so I can switch up my ammo or get better results against certain enemies.. I use vats fairly often especial when swarmed. Even without AP just to help me get a bead on a particular target.
Pretty impressive you free form fight most the time... Sounds pretty exciting!