An obvious issue is that the CSA was already decidedly weak compared to the USA. Even if both sides face issues like this, the fracturing of the CSA is likely to bolster the Northern cause sufficiently to allow for victory and re-unification.
Additionally, the notion of a Pacific Republic was always far-fetched. Southern sympathisers wanted it, and they were pretty much concentrated in Southern California. If Johnston decides to support them, you'll end up with a bit of a "California Civil War", with the secessionists being only those who are either sympathetic to the South, and those who can stomach allying with the South in order to achieve separation from the USA. A pre-emptive move will give them some initial momentum, but will also galvanise all others against them. So at best, you get a 'de facto' bulwark of Southern-aligned forces controlling Southern California.
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My proposal for getting what the OP seeks is to focus on fracturing the North, and then letting the South splinter after the war is over. This is not entirely implausible: the weakening of the North bolsters the South, but the North still had a huge initial advantage. Suppose that Johnston sides with the Californian secessionists, and a Californian civil war erupts. At the very least, this disrupts all travel to and from California, and creates a huge mess. The Union is somewhat distracted by this, leading some to aggressively question the Anaconda Plan (because the Western / Trans-Mississippi 'wing' of the Confederacy is seen as more threatening/important than in OTL.)
As a result, the Union strategy is less concerted and more dithering, especially after Johnston and his forces manage to get away with winning a pretty major victory out West. The effects back East are that the Union does worse. Specifically, the decision to re-dedicate naval forces to a
long journey to California, in order to liberate Los Angeles, is later revealed to have been a huge error: it prevents the OTL fall of New Orleans on schedule. This encourages both the Confederates and anti-Lincoln agitators up North. With the war looking worse for the North, the New York Draft Riots escalate -- resulting in a state of anarchy that isn't quelled in time for the '64 election. At the same time, the Mormons begin to exploit the situation by (informally) moving to secede (as-yet undeclared) "Deseret" from the USA.
We still see Lincoln winning a fiercely contested election in '64, but the war is decidedly dragged out, and Northern discontent mounts. Maybe the anti-Lincoln candidate in '64 had suggested some kind of compromise with the Mormons, but Lincoln's victory puts a spanner in that -- prompting the outbreak of open war in Deseret (which now formally declares independence). With the anti-war party overwhelmingly favoured in NYC, the city declares independence as a Free State. This is followed later by a Native-American revolt in (mainly) the Nebraska Territory, and then -- in '66 or so -- the declaration of independence of the Northwest Confederacy (which includes Lincoln's home state).
At that point, the Union, facing an array of enemies, can no longer maintain its war effort against the Confederacy. With the escalating number of crisis, the Union advance had already been halten, and then -- in places -- reversed outright. Thus, the war comes to an end. The CSA, being greedy as hell, insists on claiming the Upper South for itself, and the broken Union government withdraws from Missouri, Kentucky, West Virginia, Maryland, Delaware, and (most embarrassingly) Washington DC. By then, though, the problems of the CSA itself become insurmountable. The long, hard-fought war has wrecked the Southern economy. Much like the veterans of the American War of Independence, the Southern soldiers go unpaid. Mutinies ensue. Meanwhile, Texas looks hungrily at its surroundings. The way the Texians see it, the USA has been cut off from everything West of the Mississippi. Anything not already claimed by Mormons, Californians or Indians is right there for the taking... by
Texas!
The decision to annex the Upper South also backfires, when the Appalachian regions -- never all that firmly tied to the low-land slavocracy -- declare independence of their own. The inclusion of Non-Confederate border states makes all the difference there. Thus, a country is born consisting of Kentucky, West Virginia, the Eastern half of Tennessee, the Westernmost bits of Maryland and Virginia, the Northernmost bits of Mississippi and Alabama, and the North-Western tip of Georgia. Michigan, Winsconsin, Iowa and Minnesota, fearful of the Native American war-bands to the West, join the Northwest Confederacy (which rather makes up for not getting Kentucky). To screw the CSA, which did claim Kentucky, the Northwest Confederacy at once recognises the new Appalachian-based country (Franklin? Vandalia?). Meanwhile, Missouri descends into a bit of a civil war, with its Northern portion joining the Northwest Confederacy while its Southern half stays with the CSA.
Texas declares its independence claims Indian Territory, Kansas, and Confederate Arizona + everything East of the Rio Grande. Deseret claims the rest of New Mexico Territory, in addition to (obviously) all of Utah Territory. The settled, coastal regions of Washington Territory and Oregon join the Northern two-thirds of California in becoming (initially) "the Unionist Pacific states", and later "the Republic of the Pacific". The Southern third of California becomes the Republic of Colorado, and enters into a treaty of alliance and commerce with Texas. Meanwhile, East of the Republic of the Pacific, North of Utah, West of the Northwest Confederacy and South of British North America, a large area has been carved out by Native American insurrectionists.
Thus, the former area of the antebellum USA is now divided between ten sovereign countries:
- USA
- CSA
- Republic of the Pacific
- Republic of Colorado
- Native American country
- Republic of Deseret
- Republic of Texas
- Northwest Confederacy
- Appalachian country
- Free State of New York
