I think this might actually be Eoin Colfer's The Supernaturalist despite your belief about the title. The main character is Cosmo Hill, who does start in an orphanage, where the orphans are forced to be guinea pigs for various products. The girl is named Mona. Stefan Bashkir is one of the kids he winds up with. The group he winds up with, The Supernaturalists, can see bluish creatures they call Parasites that appear when people are about to die. The Myishi Corporation is eventually found to be using the Parasites to "clean" energy to create a reactor to support a satellite.
Here's the summary from Goodreads:
In the future, in a place called Satelite City, fourteen-year-old Cosmo Hill enters the world, unwanted by his parents. He's sent to the Clarissa Frayne Institute for Parentally Challenged Boys, Freight class. At Clarissa Frayne, the boys are put to work by the state, testing highly dangerous products. At the end of most days, they are covered with burns, bruises, and sores. Cosmo realizes that if he doesn't escape, he will die at this so-called orphanage. When the moment finally comes, Cosmo seizes his chance and breaks out with the help of the Supernaturalists, a motley crew of kids who all have the same special ability as Cosmo-they can see supernatural Parasites, creatures that feed on the life force of humans. The Supernaturalists patrol the city at night, hunting the Parasites in hopes of saving what's left of humanity in Satellite City. Or so they think. The Supernaturalist soon find themselves caught in a web far more complicated than they'd imagined, when they discover a horrifying secret that will force them to question everything they believe in. Eoin Colfer has created an eerie and captivating world-part Blade Runner, part futuristic Dickens-replete with non-stop action.
As Daniel B. indicates in the comments, the testing on his legs was of antiperspirants (which burn their skin).
The no-sponsors had spent the afternoon testing a new series of antiperspirants.
Their legs had been shaved and sectioned with rings of tape. The flesh between the
bands was sprayed with five varieties of antiperspirant, and then the boys were set on
treadmills and told to run. Sensors attached to their legs monitored their sweat glands,
determining which spray was most effective. By the end of the day, Cosmo had run
ten kilometres and the pores on his legs were inflamed and scalding.
The whale link is pretty much a single isolated mention as best I can tell:
Cosmo thought long and hard before speaking.
‘You didn’t fail her,’ he said. ‘The Parasites are natural. You can’t fight nature.’
Stefan draped an arm around Cosmo’s shoulder.
‘Thanks, Cosmo,’ he said. ‘That’s a nice thing to say, but whales were natural and
we sure got rid of them.’
I think your "Don't get too hung up" line is the following:
Stefan kept his eyes on the scene below. ‘A bit of advice, Cosmo. Don’t get too
attached to Mona. She is the best Spotter I’ve ever seen, but some day she’ll move on.
And to answer your question, we can cover them from here. If they get made, we can
create a diversion, draw fire away.’