The "Neptune" arrived in Melbourne at the end of March 1841. So I would think there both met there, which is where they married.
She died well before civil registration, so the most you can hope for is a church burial record somewhere. I did not find one.
Honan was granted a ticket of leave in 1840, and cert of freedom in 1841 just a few weeks after his marriage to Winifred. Information on his TOL, gives his employer and that he was off to Melbourne.