Might work, even though the Yamaha has a smaller engine. If only by a few CC's.
I actually use a standard 2" Flowmaster on the back of mine, sounds great. One nice thing on the 410 is you actually have 2 1" pipes coming off the header that don't go into a collector until they are pointed straight back to the back of the rig.
So for a new exhaust you just need some 2" pipe, a muffler with a center line inlet and outlet or even offset outlet, and two 45 degree bends.
You cut that collector then just bend your 2" pipe into a bit of an oval shape instead of a perfect circle and weld it together. From there your pipe is pretty much straight back to the axle. Use your first 45 degree bend and attach your muffler. This will angle it above the axle and keep it parallel to where the body steps up. Then put your second 45 degree bend on the top and run your exhaust out the back.
You can put an exhaust tip on it if you want. We just took another 45 degree bend and cut it flush and put it on the back. Keeps the rig a bit quieter.
When I built my exhaust, I actually used a muffler with intake on one side, outtake on the other. Then turned it sideways and used the difference to clear the rear axle. It works great but the muffler has taken a bit of a beating. And after installation I realized there was enough room to mount the muffler normally and still clear the frame. I can throw some pictures on-line if you want.
Note: Mind you, the SJ-410 has a 970cc engine where the Samurai (SJ-413) has a 1.3L
