I know. I sound like a spammer but these emails are completely legitimate email confirmations for people that have signed up for an account on this website we developed. The
Your delivery rate has little to do with your software and a lot to do with the reputation your domain and IP has with the recipient's mail hosts. Having SPF and DKIM in place will certainly help matters (and will help build reputation over time), but if emails sent from your domain/IP did or do get classified as users by junk (or you do other things that seem fishy to the providers like sending too many emails to their domain per unit time), no amount of effort on your end can overcome that.
In my experience, those factors are far more likely to trigger a junk mail designation than something esoteric about your email headers or body. Now if you have certain popular keywords in your email that's another matter :-)
Most of the major providers offer white list programs with varying conditions. You can find out about them via Google.