A lot of the academics are only looking post WW2, a huge mistake. The best period to look at is probably the late 1800s which had a GOP presidential majority but Democrats often controlled Congress. A lot of the elections were close in the 1880s and gave the GOP 51-47, 52-46 majorities in the 1890s. The problem for today's GOP is that demographics opened up the GOP's margins in the early 1900s, something that can happen for today's Democrats as more minorities become regular voters. And this will eventually trickle down to Congress as it did then.
If the GOP wins in 2016 then they could reverse their decline with young people and minorities but they also could be a one-term wreck like Carter was in 1980.
I don't see the point in looking at the late 1800s. A lot more has changed from an era when women didn't even have the right to vote.
I'm also suspicious of any model that suggests consistent close losses for Republicans, as it doesn't allow for much of a margin of error.