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What size pelican container is most suitable for holding a Suunto Tandem? How about a tandem with cover like this?

I won't need to make any custom molding will I?

This is all you need. The only fragile part of a Suunto is the capsule. The rest is solid aluminum.

IF you have the yellow rubber boot, which I have, (I also have Scott's vial covers) then the 1020 pelican case fits it perfectly and will not allow it to fall out. I use the case because of the wet muddy crap I survey. After the shot its put back in the case and the crappy crawl continues without having to put it back in my swaygo.

I don't like the yellow Tandem condoms. They protect all the areas that don't need protecting, and make it more difficult to take readings... but that's not what you asked.
I also use the Pelican 1020 for transporting. It's almost like it's custom made to carry two Tandems - one for FS and one for BS. I prefer the 1020 with the colored lid. This model has foam inside the lid, which provides better protection. I don't need a clear lid because I know what's inside.

Chad, they are not vial covers. They're quite nice, actually.

Also, are the q-tips for swabbing the lens? This may be a nice alternative to clensilingus. I prefer instrument tape.

They are for cleaning out the eye pieces and for cleaning the lense on my disto. I have taped the eye pieces before but I rarely use my own tandem. I take it for others to use but the eye sights are adjusted for me.When someone uses it (frequently) who's eyes arent like mine they have to adjust the damn eye sights, screwing up the tape so I ditched it all together. I would say "get your own" but mine and a friends (whome I survey 99% with) both shoot the same, rather than others who are 1-2* off. Using ours eliminates the need to run a compass course before i Plug the data into walls.

Thanks for the tips! I thought I had heard that I needed to keep my instrument out of the water, so pelican case becomes quick nice in a wet/muddy place like Arkansas.

Suunto instruments are waterproof as long as the capsules are not cracked. However, water/mud can get behind the lenses. Instrument tape helps with that but it's not 100%. I have never put my instrument in a waterproof container. But, I carry it in a swell, waterproof pack.