S.,
Two of my three daughters had molluscum, one fairly widespread over her body and the other only in two patches on her arm. It is a wart-type virus that spreads when the bumps are opened (scratched, picked at, or when they open themselves as they heal) and can be spread by tubs, sharing towels, touching each other, etc.
It does have something to do with immune system strength too, since kids under age 5 get molluscum more often. My daughter (4 at the time) with the widespread case had eczema also, but my oldest (7) did not contract it at all. The baby (2) had a few bumps.
What helped us: bandaids over very large or recently opened spots (I would also smear some neosporin on opened sores so they would not get infected with bacteria), antihistamine creams to curb itching, washing hands a lot (good advice anyway), and time. Keeping the areas dry is important, so perhaps try a drying agent/cream in those moist areas on your son's body.
We consulted our pediatrician and also saw a dermatologist. They offered topical creams for it, but they were quite expensive and didn't promise to resolve the molluscum any faster than waiting for the virus to run its course, which we were told was anywhere from 4 months to 2 years. It took about 12 months for it to get out of our house, and it would come-and-go in stages. None of my children's friends or other family members contracted it.
It is a VERY pestering problem, but do know it will go away! The only reason both my doctors would suggest surgical/laser removal of the warts is if they interfere with the child's functioning or are in sensitive areas- eyes, ears, genitals, etc. Apparently removal is very painful and can leave scars that look worse than if the molluscum heals on its own (neither of my daughters have scars from it!)
Hang in there and good luck with your son's allergies too... he may just grow out of them as well :-)