I haven't built a cloner like that or at all but I was thinking that maybe doing something like some how attaching a skirt around the edge of the inside of the lid might work. It would need to be secure, maybe using a hot glue gun. Silicone is waterproof but I don't think it would be strong enough to hold long. Another option might be making a new lid out of Styrofoam sheets, used for insulation and found at hardware stores. Making it so it drops down inside the container. I have found that a soldering iron works great to custom form it, and it also seals the edges so you don't get the little white balls all over the place. Or maybe even hot gluing the Styrofoam to the inside of the lid as the skirt could work, if it doesn't melt it before it cools. Though it might be simpler and less frustrating to find another container as you mentioned.
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As far as moving these guys to their more permanent sites...would you recommend I go straight into a 3" pot or so (which seems to be what the average is folks use to take their plants to maturity in a mix aero/hyrdo system like I have)...or do I need to go in steps? Like maybe to a 1" or 2" pot first...then move to the 3" later?
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Going directly to the 3 in pots should be fine as long as the roots get the moisture they need. If you use smaller pots and the roots grow through before you get them into the larger ones you will need to trim the roots to transplant it again.
P.S. I do have a plan for a simple inexpensive chiller that should do fine for that size (5 gallon reservoir). If you are interested let me know.