First of all, I completely understand your struggle. Im in the middle of recording myself and it can have timinig issues but I do have solutions for you!
Now the first thing, when you record, im sorry to say that, but feel aint your friend unless you are an accomplish pro. This applies as much to me as to you. Make the metronome your best friend. Playing with your main drum backing track can work too. But if you just hit record play your thing with no timing, no metronome or no backing track, you are shooting yourself in the foot. The other option where playing with feeling may work is in a band recording where everyone plays together but thats because you play with feeling with your drummer and bass player who do the same because you will have a concept of timing to play off of(if competent, again, wont work for any average band).
Now okay, you dont say it in your post but maybe you do play with bpm or with a backing track. Then indeed, it can be tricky to have them both play each other be the exact same way.
Truth is, they wont be exactly the same. Doesnt mean you cant make them tight. The best advice I was given, which I use as we are speaking, is to do your first rythm guitar track, pan it completely to the left. Then go to your second guitar track and again pan it completely left before you hit record. Once you record, you will basically be playing over your initial track and will then be able to really hear how tight it is and really have a feeling of guidance. Once happy with both performances, voila.
Recording is hard. that red light thing can add pressure. But once you relax and wont feel pressured anymore and have fun recording, you will see results! Dont push yourself too hard and take breaks if you get frustrated. Misplaced anger will not help!
Hope this helps, let me know if either it wasnt clear or if needed more advice!