We had pretty much the same issues. 

I did speak with DoR this morning and confirmed the same thing, can do the combined federal program unless they have withholding. IRS doesn't send WI the 1099's until April.

We did upload a few through My Tax Account (more than 10 1099's) last year but that is a huge pain. All said and done, we mailed off a bunch last year just to be on the safe side.

I haven't decided if we are going to do the same thing this year. But yeah, what a mess.