The Confederate 'invasion' consisted of a very tiny force, little more than a thousand men on each side. Why? Because a larger force could not be supplied off the land and there was no railroad. Indeed, Sibley's force nearly disintegrated from lack of supplies after the battle. It wasn't from lack of interest: seizure of the California gold fields would have financed the Southern war effort. There were enough men of Southern ancestry in California that the state legislature had petitioned Congress to divide the state in two, but the Civil War broke out before it could be acted on.
Before the Transcontinental Railroad, moving troops to the West Coast took forever and was very expensive (civilian passage took about six months and cost roughly $1000 per person - a very large sum in those days). The usual route was by ship because marching overland killed men and horses, and stirred up the Indians too. See the Memoirs of US Grant for the horrors of this trip.
The railroad could carry its own supplies (even water) and could make the run from Omaha to Sacramento in less than seven days (five IIRC) for a cost of about $100 per person. It was financed with enormous land grants, government direct payments per mile and bonds issued on government credit. Despite the horrendous cost the railroad turned a profit and the government saved more IN ONE YEAR on troop movement and supply costs than it spent on the railroad!
Fun fact: when chartered, the Union Pacific and the Central Pacific became, overnight, the two highest capitalized and largest corporations in the world... and they both nearly went broke trying to get it built. The job required thousands of men, expert logistical and supply and massive amounts of material. Please remember even the first crude railroad across the country was built entirely by hand with black powder, shovels, picks and hand-powered drills.
There shouldn't be a link from the southwest to California unless it requires six months and attrits the force by 33 to 50 per cent.
