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When I load my Ultra on the trailer I bend the antennas over and lock the tips in the Tourpac latches. You just open the latch, put the antenna tip under it and close it. Left side antenna goes into the rear latch and the right side antenna goes into the front latch.
If I was going to put a cover over the bike I think I would take the antennas off.
I have the HD cover for an UC with the slot across the back that the antennas stick up through. I let them stick up. I got tired of having the 06 UC scrape the top of the garage door when I go in and out, so i bought the J&M shortys.
I used to bend them over and stick them in the saddle bags latches, that was until the day I was riding back from someplace and noticed something was missing in the right mirror.
Antenna broke below the load spring and the mounting point (that little short piece of antanna there). Parts guy was more than glad to sell me a new one, and commented that "I bet you bend them over all the time".
I said "yeah why"
He said "we sell alot to you guys that bend them over, you do know the Harley cover has slots for the antennas"
I said "Yup"
On the less expensive covers without the antenna holes, mark the spot with magic marker.
Have your wife (or whoever) stitch around the area with a sewing machine,
Then using a hot nail or such, melt a hole through.
The hot nail seals the threads to stop unraveling and the stitching reinforces the opening.
I have a seamtress in town that does all my sewing needs including chap and leathercoat zippers and patches.
She is reasonable and does a good job.
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