Hi Tom,
The starting point for the documentation can be accessed via the link at the top. See the MJLJ V3 section. As you will see, much of the information covers the construction of an actual MJLJ unit. You will need to review the last step, covering vehicle installation.
This is where the instructions end, and as you and at least one other person pointed out, the rest may be non-obvious. So we certainly need a few more sections to get you to a working installation.
These are the basic steps required to get your MJLJ running:
1. Install the Ford EDIS system and verify it is working on your engine. see the information library and the other technical info, links above. This involves installing an appropriate crank trigger wheel, crank sensor, coil packs and the EDIS module matching your engine configuration (4,6, or 8 cyl.)
2. Once you have verified the EDIS module is controlling your ignition, you can wire in the MJLJ. See the <a href="/mjlj/?q=node/606">vehicle installation</a> section.
3. install the configuration software, connect your PC to the MJLJ using a serial cable, and start tuning your engine.
Here are the answers to your specific questions, and a bit more to get you started:
The completed unit you received already has the firmware installed- no need to worry about installing bootloader/firmware. On the included firmware is a 'safe' ignition curve that should work fairly well for most engines.
Download the configuration software (See 'software' link at the top). There is a quick readme included with this to get you started. Note the default firmware is configured for a 4 cylinder engine. If this is not what you have, you can use the software to change it.
The 'high' vs. 'low' on the outputs refer to the behaviour of the output when the configured threshold is crossed. If it is configured as 'high' the controlled device will be enabled once the configured value is reached. If 'Low' is selected, the controlled device will instead be turned 'off' when the threshold is crossed.
'high' and 'low' is a bit of a misnomer, it really means 'normal' and 'invert'. Here's a concrete example:
You have a LED lamp controlled by user output 1, and You want the LED to turn on at 4000 RPM. You would configure the output as type 'RPM', value '4000', and mode 'High'.
If you changed the mode to 'Low', the LED would be on below 4000 RPM and would turn off at 4000 RPM and above.
I hope this helps for now, I think your question has prompted me to do a round of documentation enhancement!
Regards,