I have a thought on why the father James Malloy is not listed on the 1880 census. The family came to Atkinson Nebr in the spring of 1882, James may have been on his way here to stake his claim for a homestead, some of the rules were that it had to be occupied and a sturcture had to be built on the quarter section of ground. This would have taken some time, I would think in those days to travel from Penn to Nebr, get things squared away here and get back there to bring them here. It's the only reason I can think of.
I know for a fact that James , Margaret(MaNally) and some of thier children came to Atkinson Nebr in the spring of 1882. The children that came with them were John , Charles , Maggie Ann (my great grandmother) , Thomas J. , James J. (your wife Mary's great grandfather) and Michael. The oldest child was Bridget who didn't come with them , she may have been married at the time, she wound up in Utah, she married a VanRansel (not sure on the spelling) they had one daughter Geneveve. This is what I was told by the lady here that kept in touch with Mary (May) Trankel in Montana.
I am still searching the micro films of the old newspapers here in hopes of finding an obit for Margaret Malloy, it may say where in Ireland she was born. I know that she died Jan 16, 1910, this is from the St Joesph Church records. But have been unsucessful as of yet because there are some issues of the local paper unaccounted for, but while keep trying.