Click here for a list of animals that have been successfully cloned.
I acknowledge that it is a monumental task to control for so many variables. The concern you mentioned that is most dangerous to my experiment is socialization. I agree that introducing free agents into a controlled environment would be impossibly hopeless. One solution I'd propose to negate that concern is to place the subjects in isolation. I also recognize that a great deal of information has been successfully extracted from other studies that failed to control for every variable. The data can still have value. Statistics can also be utilized to make inferences and draw conclusions.
The ability to communicate with the subjects would be invaluable. I agree that it would be impossible to meet most/any of the ethical guidelines of the sciences when conducting this experiment on humans. Fortunately, in the name of expanding our knowledge, our moral conscious allows us to conduct such experiments on living beings other than humans. The subjects could be simple celled organisms, mice, monkeys, other.
Subjects whose life cycles are very short would provide a couple of benefits. It would reduce the amount of time that mistakes in the proposed methodology could be unintentionally introduced. If mistake(s) were identified, the subject could be disposed of with no concern for lost time or capital.
Okay, you are willing to use non-human animals which helps with the genetics and parts of the environmental standardizations. But your proposed sample size is way too small to provide statistical power to detect the differences you wish to detect. You probably would want to start at with at least 10 times more. But separate from the size of the test population:
One doesn't have to bother cloning a number of species: one can easily buy genetically identical mice for example. Cheaper. But the non-genetic variables still make this an absolutely impossible experiment.
Some mice moms produce (depending on the strain) 4 to 17 babies each, so to study the numbers you need to you would have to compare individual mice all birthed on the same day but born to, and raised by, several different moms (you can't separate new born mice from their mom's until after weaning). Being raised by different moms will result in very different weights, physiologies, behaviors, etc. in the different babies that will persist in different ways into adulthood. A known variable that cannot be controlled for.
Even genetically identical babies born to the same mom at the same time differ from one another in detectable ways (i.e. mice with blotchy coats have the blotches in different locations even if they have identical genes, or the birth weights will differ somewhat for the different babies) due to random effects during development: position in the womb, expression switches that fall on way in one baby and another way in another baby, etc. Another known variable that cannot be controlled for.
Okay, you have gotten the mice through weaning and will put them in identical environments. How do you propose that? Stack their cages? Then the cages are at non-identical heights and probably temperatures. Place the cages next to one another? Believe it or not this makes a difference too. It is very hard, especially if studying many mice at one time, to keep the environment absolutely identical for each. Certainly they would all have to be in the same, large room and different parts of that room will have different air flows and slightly different temperatures. Are are the watering systems delivering water at exactly the same pressure? All the food being meticulously replaced by the staff on all the cages at the same time. Do all the animals see the same things so they are soothed or frightened the same when an investigator comes into the room? I presume they cannot see one another because there is no way all can see everyone els the same way, and this has known effects too. More known variables that cannot be controlled for.
I could go on but I think I've illustrated the point. Mice are probably the easiest mammals to try to standardize genetics and environment, but one simply cannot do to the extent your experiment would require due only to the known variables that have nothing to do with consciousness. I know: I've worked with genetically identical mice and I know what can affect the results and how to reduce these variables to the bare minimum. There is no way to eliminate these variables.
Further of course if you were to somehow eliminate all the known variables, revealing an unknown variable only does just that, revealed an unknown variable. Slight differences in light intensity? Differences if the cages are near a wall vs in the center of a room? Etc. Your proposed interpretation would hardly be the default explanation.