It might have been better to extend extra runners to the cap from the main sprue, rather than trying to flow plastic into the main body, back out again, and into the cap. Then you could use submarine gates and eliminate all the trimming. Probably too late for that now.
Maybe a hot knife, or a vibrating knife, but it's still skill- intensive and needs to be done under magnification, which is itself exhausting. At least buy a television based microscope.
Sellers of ultrasonic machines will mumble sunshine promises. It never worked worth a crap for me; maybe your mileage will vary. Insisting on a money- back performance guarantee for machine and tooling will considerably cool their ardor.
Could you weaken the ends of your pseudo- runners so that you can snap them off at assembly? Or make them flexible enough to leave in place? Yeah, you should be so lucky.
Or, weaken them _away_ from the body and cap, so when you cut them or snap them, you leave a stub on the actual parts? Let me guess; it would be a puncture hazard, or would interfere with some tight clearance.
Sorry; I was in a bad mood _before_ I looked at your problem ... and I don't see a magic bullet anywhere for you.
Mike Halloran
Pembroke Pines, FL, USA