1) Right now I'm playing game after game as the CSA, and while I can crush the Union if I blitz them I'm having trouble with the fact that EVERY SINGLE PROVINCE I own has a revolt risk of 1-2%, sometimes more. Needless to say smashing the North while the South slowly turns black is very disheartening.
2) Another issue is that if the war drags on into 1863 (which happens if I try to get the border states like Delaware and Maryland to secede), the Union will suddenly spawn over a dozen full-strength divisions and maul the crap out of me (this happens SR or not, but the following seems to only happen with the mod installed).
3) Further, the Union will ALWAYS choose to continue the war if the House Divided event fires after this point, and the Yankees seem to have the magical ability to capture provinces in two or three days with a single division, with control rates going up by 20% or more a day. This leads to most of Virginia falling in the time it takes me to (re)capture Pittsburgh or Washington.
4) Edit: Oh yeah, one other thing - SR puts some other general in front of Robert E. Lee, which means you have to spend 40 leadership to get to Lee and the new guy has a tendency to take over Lee's command if their armies get merged for any reason, due to his 'seniority'. He's too valuable to dismiss, so I'd suggest moving him to second place after Lee (even if it isn't completely historically accurate), if only so that I can put Lee in command of the Army of Virginia immediately instead of waiting for my leadership to refill.
1) One to two percent revolt chance is not unusual in wartime, and can be influenced by a dozen things unrelated to the mod--taxes, for instance. If you're fighting into 1863, War Exhaustion is also taking its toll on your people just as it did IRL. Also, SR (unlike vanilla) simulates how unpopular conscription was. If you enact a draft, that's going to anger everyone but the upper classes. Again, that's historical, and that's what SR is about.
2) You're trying to do something that--from a historical perspective--is risky, to say the least. The South isn't going to win the war going after the border states (*especially* California!) unless things are *really* going well for you, as in "better than I've ever, ever seen them."
I think the crux of your problem is you're overreaching and trying to do way more than an agrarian slaveholding nation can reasonably be expected to do against a relentless enemy with far more people and industry. Sure, we'd all like to press on to the Canadian border

, but it's just not possible in anything even vaguely resembling the real world of 1861.
My advice would be to try to win your independence at the start, and leave it at that. If you really have designs on MD & DE, get them at the peace table. You're beating enough long odds just by winning independence.
3) I strongly recommend a save and reload after DC and Philly are in Southern hands. That way you have the option of re-reloading if the Yankees don't quit.
There's only a 4% chance of the Yankees refusing to make a peace offer, with or without my mod in place. The above suggestion should deal with that slim possibility in the future.
4) Not sure why you can't just remove A.S. Johnston whenever you want, or why you'd have Lee and him anywhere near each other. In any event, the fact was Johnston ranked Lee, and thus it shall remain in SR.
Just a final reminder that SR isn't about making the Yankees saps, it's about making the War more historical and the postwar Confederacy more interesting. The Union crushed the South, and should continue to do so in the game unless the player is skilled enough to throw history on its ear.
The good news is if you scale your efforts back to what's historically feasible, you'll win the South's freedom and can go where you will from there. Remember: today the Yankees, *tomorrow* the world.
Thanks for trying SR--I hope it will be worth your investment!
Edit: jamhaw is 100% correct about Cali.