Is there a 6309 simulator that lets you single step and see he registers? There are emulators for the CoCo3 that uses a 6309 but they don't really seem geared to writing your own assembly and testing it. Any suggestions?

You've probably already spotted it, but if not:
There is source code for "Lex's 6309 simulator" listed on the following page.
http://www.sdc.org/~goosey/

Direct file link:
http://www.sdc.org/~goosey/unix/6309sim.tar.gz

It looks like it'll need a bit of work to get it working on little endian architectures,
but might be better than starting from scratch if that turns out to be the only other option.

The 6309 is an expanded version (superset) of the 6809. A number of simulators and emulators for the 6809 exist.
I found a few webpages by addressing "6809 emulator simulator".
It doesn't look like there's a lot in the way of 6309 simulators. It may be necessary to modify a 6809 version.

If you have access to a 6309 core (VHDL / Verilog FPGA for instance) you could run the core in a test bench in a (generic) logic simulator. That would provide the ultimate control for stepping through software, but it's a slow going process. I've done initial software debugging for a number of cores that way before the software gets too complex.

I was just having a look at the rtf6809 today but unfortunately I didn't get as far as writing a simulator for it yet.
6809's one of my favorite processors, but not the 6309 so much.

Thanks for the suggestions. I thought about trying to write my own simulator, but from the datasheets it looks a lot more complicated than something like a 6502. I'm also not keen on rewriting someone else's simulator hoping to get it right. The 6809 assembler/simulator on ASM80.com works ok (it hangs on DAA, for example, and the 6502 emulation is broken.)

In the end I found an assembler called lwtools and got it to assemble a 32k raw binary file. I can overwrite the coco3 ROM and do a hard reset in the MAME emulator to get it to reload the file. It works well enough to see all the registers and single step.