Hey Bradley nice to be back in touch with you - looking forward to more chatting via IM!
Regaring stainless filler rods, I haven't done enough back to back testing of stainless filler rod to be really certain about the differences of 309 vs 308. But here are a few facts I can offer about them based on what I've read and to a limited extent, from my experience.
308 is "technically correct" for welding 304 to 304, so you should be all set to go with it.
309 has a higher nickel (~12%) and chromium (~24%) content than 308, and so generally costs somewhat more per pound. You will see it generally called for when joining "dissimilar" materials (such as mild steel to 304 stainless.) My hunch is that the higher nickel content increases elongation & ductility, and makes it more suitable for joining materials that expand and contract with heat at different rates (such as, stainless to mild, or one stainless alloy to another stainless alloy.) But I think another reason the 309 is called for is the higher alloying ingredients can be "diluted" with a lower alloy parent metal and the resulting diluted weld bead still maintains enough alloying ingredients for acceptable corrosion resistance and ductility.
Now I've used 309L for joining stainless to "same alloy" stainless, as well as for joining mild steel to mild steel, and I can't find anything wrong with it based on the way it welds and holds up. I think the reason its not "recommended" for these application is because simply that other less expensive filler rods are available that do these jobs satisfactorily (such as, 308 for joining 304, or 70S2 or 70S6 for joining mild steel.)
However I've noticed something I like using about 309L to join mild to mild - it seems to dissolve oxides very well, and not leave anything floating on the surface, giving a really fluid, easily controllable molten puddle, as well as a great looking weld deposit. check out the attached picture, 309L joining cold rolled mild steel together. The puddle is really fluid. I've heard the nickel is what gives the oxide dissolving qualities. Sort of like a built-in flux that needn't be cleaned off afterward. 308 might work well for this too but I haven't experimented much with it for welding mild steel yet.
I've heard from others that 309 works really well for welding dirty steel (like hot rolled mill scale), although I haven't had opportunity to try it on that yet. Maybe kind of like a built-in flux that doesn't need to be cleaned off afterwards.
(The "L" suffix means low carbon by the way, and generally increases ductility of the weld deposit at some loss of tensile strength - usually but not necessarily always a desirable thing IMO.)