>>1. i am going to build a step pyramid for the uros to use as a
>>basking spot (with several varying heights) and was wondering
>>what is the safest way to glue the stones together?
I would avoid applying anything to the stones like you're thinking. First, probably all compounds that "cure" outgas in some way. Many of these fumes can be fairly nasty (don't inhale). Second, when you start introducing adhesives to things like this it eliminates teh possiblity of sterilizing the components in your oven. I've also found mites (and/or other insects) will live between flat stones or tiles. I'm systematically eliminating them from my enclosures... for supports I now tape three small bathroom tiles together in a triangle and use sets of those to support larger flat tiles. If you've ever deal with mites or other parasites in one of your containers you'll appreciate this.
>>2. the enclosure is nearly done aside from needing to touch
>>up the paint in a few spots (i used non-toxic paint). At the
>>bottom, there are a few spots where there are small gaps
>>between the bottom and the sides and i was hoping to seal them
>>with some sort of sealant....
Worse than migrating seed is the potential of pest infestation. Those areas match my prior description of hiding places for bugs. I used epoxy resin to seal all interior wood surfaces and fill all gaps of the UroCondos I built. Epoxy resins have the advantage of a known and very finite cure time during which outgassing occurs and thereafter ceases. In one part compounds (including paint) your cure time has a lot to do with the air exposure, hence the reason a bottle or can of the stuff doesn't automatically solidify. As a feature for epoxy, at final hardness you're looking at a surface as hard as aluminum, so essentially impenetrable by the animals.
A rubber squeegee is prime for spreading epoxy over large surfaces, disposable or "acid" brushes for application to small areas and thorough stirring. Epoxy sets with a longer cure time are normally thinner and easier to spread (penetrating further into the gap by capilary action) while also being stronger and less brittle in the finished product. The downside is, of course, if you don't mix the resin properly (adequate stirring or wrong proportions) you will end up with the "stuff" never curing so test ahead of time.
Cooler temperatures will induce longer cure times in any resin mixture so a "faster cure" mixture could end up being slow cure in a winter garage or work room. Leaving the resin in the "pot" with little volume surface area versus spread out over a large surface will induce a faster cure time (and potentially ignition in large enough volumes) so make sure you mix thoroughly for a couple minutes and then apply and spread.
To do four 2x4'x18" cages I bought something like three gallons of resin and probably used less than 16oz. If you wanted to try this a resin kit from a hobby shop that's about $10-$15 (price dictating volume because I can't remember the measures) would be about right and probably excess.
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uromastyx geyri (Saharan/Nigerian), hardwickii (Indian),
macfadyeni (Somalian), ocellata (Sudanese), ornata (Ornate), benti pseudophilbyi