I have successfully removed and replaced the crumbly caulk.
As a further improvement over the repair job I made on the window boxes, I cut out some discs from a couple of plastic food container lids, and used those to seal either side of the repair job, instead of leaving the silicone exposed.

To help ensure a good seal when drying, I used a couple of bricks, some parchment paper and 3 bags of pebbles to apply some weight/pressure while curing.
The challenge came from the ridge running down the middle of the inside of the box, as it caused anything placed in the box to seesaw either left or right preventing me from getting an even distribution of weight. Insread, I placed a piece of parchement over the plug, and used the pebbles to apply pressure while it dried.

As the exterior bottom of the window box was smooth/flat, I was able to rest it on a pair of bricks, to apply pressure, when curing

After getting the window box patched (I only patched 1 of them) I moved back to the irrigation lines that I wanted to finagle into the pump.
I figured I’d make 2, just in case I need a backup.

There was nothing fancy to my technique.
I used a couple of rubber bands to hold the irrigation lines together (on one side), then squeeze a little silicone in between the 3 lines, on the other side.
A 3rd rubber band was added to hold the siliconed side together, and the oozing silicone was spread with a popsicle stick to achieve an even coating, holding all the lines together providing a seal when inserted it into the pump.

The final thing I did, while the caulk was handy was seal up a couple of nails and rare earth magnet. I want to experiment with using something similar to a stir plate as a means of moving the growing solution around, so I need to make sure that the metal isn’t going to be able to react with anything.