Hi there. It's not a problem. Here are some tipps to get that NIOS Code running. First to tell you, you are totally right. The Nios EDS codes many paths hard into the bsp. I also have problems with that every time I get a project from a colleague.
My way (perhaps not the best way, but it works) is to generate a totally new Nios Project. Generate it from template, with bsp. I always take "hello world" as template. When the generation is completed, you will have to edit the bsp settings. In the first tab you chose the ssram for the two stacks. Then in the linker tab you set every property to ssram. After that generate the bsp.
Now the last thing to do is open the previous c-code file in your favorite editor and past and copy the code over to the new hello world c-file. When you then compile the whole code it should work fine with my synthesized system.
I will also have some sparetime over lunch, where I will test your hint with the sequential transmission. I really never thought about that, also not read it in any documentation I think, but that seems to make sense. Will have to try that on the hardware.
(btw. it's not your problem, that I bite something like this question so much. This even helps me very much, because when we get that system to work with the CVO it will help me for an old project. So don't let yourself wear down by it.) ;-)
Yours, Peet.