Actually the transcontinental railroad wasn't completed until 1869. The first track for the Central Pacific was laid in Sacramento in August, 1863 and work on the Union Pacific didn't start until July 1865. And work on the Union Pacific was slowed because of the demand for railroad supplies caused by the war damage to the existing rail infrastructure in the US.
And westward expansion slowed considerably during the war--logical since most of the men who would have moved west were otherwise occupied. It picked up again after the war, thanks to the Homestead Act and a provision that waived a portion of the residency requirements in proportion to service in the United States Army.
Seems that a major project like that would be put on hold by a country with no arms and legs bleeding to death.....