Hey Nathan, Really the training is probably the most important issue here for adding muscle to your body (assuming you eat enough calories). 3500 seems like a very reasonable number for a healthy active adult male. You can use cronometer.com (it's free, just plug your food in) to get a good feel for what you are currently eating and then you can really just eat the foods you like in the quantities you want and just shift their ratio's around some. You sound like you are eating whole unprocessed foods for the most part, and apart from getting a feel for things I don't think it necessary to count and delegate every macro/calorie if you just want to look good and get strong. If at some point you want to compete in bodybuilding or strength athletics then it may become more significant.
With the squats I'm somewhat timid about giving you direct advice because I don't know the extent of your injury or pain. But in my experience people with lower back injuries at the very least are able to perform box squats without great pain. And as the lower back muscles become stronger they usually find that they have less pain over time.
2 pretty good resources of information that you might try is messaging "veganessentials" at this site. There are other people here that have great information, but he has personally given me some pretty good tips on fixing my squat when I've posted small issues. And Kelley Starrett is a physical therapist that has written a great deal about biomechanics in weight lifting. He seems like a little bit of a douche, and he's really into "Paleo" dieting, but all that aside he seems nice and he's a wealth of information in biomechanics, so reviewing information at his site http://www.mobilitywod.com/
(just search "lower back pain") might help you trouble shoot why you might be experiencing pain and provide you with tips and ideas on how to progress and improve.
Hope that's helpful, and yes please keep us posted on your progress.