The HRC card isn't supposed to work with the stock loom at all. To do so would have provided too easy a way round the 40bhp Jap domestic restriction.
Honda would not have been allowed to sell a different "key" which raised power by about 20bhp and blanked the speedo out!
Even buying an HRC card back in the day in Japan used to be hard, you had to provide a race licence.

Removing the sidestand and neutral lines (which are the ones that go though the PGM itself, it's for the side stand down while in gear cut out) fools the PGM into thinking it's running on the race loom.

And yes the stock card will still work, but if you jet the bike for the HRC card the stock card will run terribly. If you don't the HRC card will run terribly.
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Please do not PM me technical questions, if you can't find it on the Forum start a thread