Is the collar attached to the lid or to the freezer? If the collar is attached to the lid I found it easier to do everything else (drill and mount the shanks/taps, install insulation, mount secondary regulator, etc) first then put the top on last.
That clear caulk is plenty and you should place it, squish it around a bit to get good coverage then drop some books or something on top to weight it down and leave it at least over night.
With the lid attached to the collar it really never takes any stress so I've never had a problem with mine. If you grab the lid and lift it open that way it might be more of a problem though. That is why I put a towel rack/handle on the front of mine.
The link to my build is in my signature if you want to see how I went about it.
Oh and there is a whole DIY section... you'd get more response if you posted this there. I would imagine a mod will move it when they see it though as it really belongs there anyway.