I feel that having great rhythm as a guitar player is all too often overlooked. I spent most of my guitar playing life focusing on that as opposed to being a lead guy. That practice came much later in my playing.

The best thing I can recommend is practicing daily with a metronome, and also make sure you are playing with other people that have good time. A great drummer can really show you a thing or ten about playing in time. It sounds like you are in the company of some good musicians, so why not join them if you can?

Drum machines also helpful too. There are a wealth of programs and apps, free and paid, that can help with this. Make this a part of your daily routine and it will come together.

If reading rhythms is something that you think will help (which it does), I recommend this book. It's for drummers, but can be used by any musician. Good luck! :D

Encyclopedia of Reading Rhythms