And given that you have fewer than 60 riding days.
A direct route from Oregon to NYC would seem best.
If you are flying into SF, you can take Amtrak to Eugene, Oregon and connect to the coast.
Or you can fly into Portland, Oregon and connect to the coast from there.
A direct route would start on the TransAm - plus you would have benefit of bike route services.
Then a route across Idaho thru the Sawtooth Mountains and Stanley - beautiful!
Then on to Yellowstone NP, the Grand Tetons and across Wyoming.
(Most two-lane highways in the rural West have low traffic - especially Wyoming.)
If you follow the state line between South Dakota and Nebraska you will reach part of the Lewis & Clark Route.
Then you should cut across Iowa to Muscatine and pice up the Northern Tier.
(Personally, I think you should take another route so you can see Lake Michigan.)
If you cut off of the Northern Tier in eastern Ohio, you can pick up a route across northern Pennsylvania.
And then you can come down the Delaware Gap into New Jersey and New York.
It WILL require some planning to do all you want in the time you have to do it.