Disclaimer: I am still technically a pre-med, so other, more savvy members, may know better; this is personal opinion.
I was totally sold on the research option (because of your 2,000 PT clinic hours; no more clinical exposure needed) until I read
@shisong 's comment.
I'm torn now because if ADCOMs just see it as clinical experience, and don't think anything past that, you should definitely do research (no doubt in my mind.) This will allow you to at least say you've tried research, and you'll be able to explain whether or not the you liked it if they ask at interviews using personal experience. It may be a good idea to contact your top school choice and see what they think?
If however, ADCOMs ask what you were doing working at a PT clinic instead of somewhere that would get you more exposure to MDs/DOs... I ask you, OP, if you were there because you maybe thought about doing PT in the past? If so, you'd have to justify why you'd rather be a physician. In that scenario, I think as long as you're able to explain you changing your mind (using experiences you've had in the past with physicians), you'll be fine.
If you were there just because you were able to land a job (any job) in healthcare, I would be prepared to justify wanting to be a physician instead of a PT by using your OTHER experiences (shadowing, volunteering, etc.) that you've had direct contact with physicians to explain why you KNOW you don't want to be a PT, and you do want to be a physician.
If you worked in the PT clinic and don't have other experiences with physicians (volunteering, shadowing, etc.) to be able to justify why you KNOW the lifestyle of a physician is for you, I would advise taking the scribe job and explaining to your pre-med adviser that you won't be able to handle all three (scribing, research, MCAT), and that the tremendous amount of direct exposure to physicians you'll have as a scribe will likely help your medical school application tremendously.
TL;DR: Take the research experience UNLESS you can't explain WHY you would rather be a physician (over a PT) USING other experiences you've had with physicians (shadowing, volunteering, etc.)
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