You'll be fine. A few honors and HPs and doing well on step 2 will put you in good standing for almost all top tier psych or neuro programs. Just craft a package that exemplifies your strengths.
I disagree, unless you're applying to some of the surgical specialties or a community program, a PhD is seen as a positive asset in most settings. Now a PhD will not overcome a poor clinical performance.
I'm applying IM. I had 3H, 4HP, no AOA/GHHS, 270+ step2 and so far getting decently competitive interviews.