Difference in feel between two almost identical guitars?

Of course they feel different.
I would wager that they sound different as well.

It is not in your head.

These 2 guitars have different fingerboards.
These 2 guitars have different finishes.
These 2 guitars have different backs.
One of them has uncovered pickups.
The other has covered pickups.

How are they "almost identical"?
Great point.
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Definitely not in your head. If I were in your shoes, I would snag guitar 2, regardless of the color. Getting that same model in a different color doesn't mean it's going to feel just like that guitar you bonded with.
Unfortunately this!
I have a few guitars I don’t like the colors/tops of, but I keep them because they ‘felt right’ to me.

As Bodia says, snag guitar 2 because that’s the one that speaks to you.
One summer (many moons ago) I went to the carnival for the area where I went to school. I had finished the last couple of years in another county. At a booth in the carnival was the prettiest girl in my class when I was there. I struck up a conversation with her and asked her out. She said that she always wondered why I never asked her out while I was in school. (It was because I considered her WAY out of my league) I took her out, and we had fun for a while, until I discovered on that first date that she had no personality and relied on drugs to “really have fun”. Lesson learned. Looks ain’t everything.
Each guitar has its own soul. That gives it a unique feel and tone. I tell people that when I do a setup on a guitar, I set the action to where the guitar wants it to be set. Each guitar has a setting that just feels easier to play. I set everything to measurements that I know will get me into the ballpark and then start fine tuning from there. I also like to say that they all have their individual personality, just like we do.
“Each guitar has its own soul”. Perfect and so true……