What would have happened if the South industry wasnt so heavily based on agriculture ?
That would have changed quite a bit in terms of commerce.
-> Had more factories and production methods available to them.. not as big as the North, but say ~ 1/2 the North's per-capita production pwoer?)
That's a pretty big change, they would require a much more urban population. If the South was closer in terms to commerce to the north then it is likely that the huge rift that existed between North and South would never have formed.
And thus had an army that had industrial might supporting and maintaining it.
Again, we would have to add population to the mix, not just industrial might. Again, this would change the culture of the south and make it closer to the culture of the north ...
Would the Union have consented to their demands?
Doubtful, keeping the Union in tact was essential for the survival of Washington.
Would the North have lost, or been beaten into submission and negotiation ?
Certainly the South would have done even better then they did but the truth is, the population and industrial might of the north was just too great to overcome.
If so, would the policies of the USA be made by the South?
(if so, how long?)
No. There was no chance for the CSA to overcome to the Union, their only real potential was to insure the existance of the CSA.
Would the CSA have permanently gained independence?
(and the aftermath in the USA?)
If the CSA had gained its independence then there would simply be no USA. Odds are there would be a New England Alliance, some midwestern alliance, the CSA, the Californian Republic, Cascadia and Mexico would be much larger. Or, the Canadians could have explanded into the Dakotas, Oregon, and possibly further south ... who knows?
Would the USA remain a union - but even less centralized?
There would probably have been some North American Federation coming about in the late 20th century, not unlike the EU. Till then though, the different states (not US states mind you, just the different theoretical states that might exist) would have fought over this resource and that resource, not unlike what happened in Europe.
The Republican party itself also had anti-immigrant and anti-Catholic elements.
None of which stopped the use of such people in the Army. I might also point out that the Irish/Catholic wound up being incredibly influential in the North East of the USA.
The story ends, it just ends.