I'm working on a digital gifting platform that relies on email reaching the inbox. Email is sent through Amazon SES, and has high quality (recipient's name in the email, single recipient, personally crafted message, extremely low bounce and complaint rate). However, I am still seeing very mixed results as to spam filter behaviour. Some get marked as spam some don't on the same ISPs.
I currently have no DKIM, SPF, or Sender ID set (http://docs.aws.amazon.com/ses/latest/DeveloperGuide/authentication.html)
Is there any downside to using all of these together, or should I pick and choose?
Your problem seems to be here:
You definitely need SPF records to send email reliably from AWS. Due to ease of use, EC2 would be a spam haven without SPF. See this SO answer which describes how to configure SPF for use with EC2. Don't forget to fill out this form to request that Amazon remove sending limits from your EC2 instance.