It helps to practice scales while singing the notes. Play the scales in 3rds (up one, down the next) while you say the names of the notes, i.e. C-E, F-D, E-G, A-F, etc. Then do it in 4ths, 5ths, 6ths, 7ths and 8vas. Then play and sing it in reverse order (down one, up the next). This requires a lot of brain work and it's absolutely tiring. It may feel like your brain hurts a lot. But worry not that's a sign your brain is expanding. Do this for couple hours a day for a month and you'll recognise each note on the fretboard pretty much instantly. Also saying the names of the notes as you play them in this fashion is great for ear training, you may find that after a while you can hear the names of the notes just by hearing someone play them. As a plus, consider getting the book "Advancing Guitarist" by Mick Goodrick and play the exercises on voice leading the triads. These will force you to think of 3 notes on the fretboard at time rather than just one. It's quite hard to do but the rewards you may rip from it are definitely worth it. Hope this helps.
Hey Corey, I know very little but I had a similar experience to yours recently. So some metronomes have a different click on beat one. Have you tried them? It worked out for me because I couldn't focus only one beat one while ignoring beat two. The different sound on beat one made it way easier. Once I got the feel of the rhythm changing to regular metronome was no big problem either. Hope this helps. Cheers!