When I did my PPL(M), I was borderline fail in my technical exam (and had some great arguments en-route). This was just over a year after graduating with a degree in aerospace engineering.
When I did my JAR PPL, by then I was a chartered aeronautical engineer ditto. I recall particular problems with terminology on systems that I knew how to design - but didn't know the approved CAA way of talking about them.
By the time I did my CPL, I had a PhD in aeronautical engineering as well. By then I'd learned: just learn their words, their way of thinking, and accept that's what you need. Don't try to be clever, that's for later.
I also heard of a GP who may have been about the only person ever to fail the human factors exam. The rest of us, without that specialist knowledge, found it really easy.
Add into that that MS Flight Sim teaches many things from a gamers perspective, not a pilots. Visual attitude is just about everything, not instruments; system management, cockpit management and communications are paramount, whilst they pretty much sort themselves out on FS.
So, basically, you are learning everything for the first time - your FS time has little value. Just accept that and enjoy learning.
G