The Arduino firmware only really works properly at 8MHz or 16 MHz. You should be able to get a pile of 8 MHz resonators at a reasonable price and replace the odd 7.37 MHz ones. If you don't make that change the serial I/O may be far enough out of spec that you can't use it.
You don't need to worry about a bootloader. Use an ISP device (under $10 on eBay for the USBasp) and connect it to the ICSP pins. Then you can use "Upload Using Programmer" in the File menu to upload your Arduino sketches. Depending on what pins connect to the stepper you might be able to use the standard Stepper library as-is.