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This guide requires the following software;

MegaTune download from here
MSnSE (either the standard or the Hi-Res codes) MSnSe 029v, or MsnSE Hi-Res (link broken- see update below.)
and EasyTherm download from here

update: You can always find the latest & greatest build of HiRes code in the first post of This Thread at the msextra.com development forum. Note that you must be registered and logged in at msextra.com to view this thread. (Perez, 16 Sep '08)

Step 1
Install software onto your laptop.

Run the installation software for both MegaTune and EasyTherm and allow the software to install to the default locations.

Create a File called "EFI" on your C Drive and copy the zip file of your desired version of MSnSE into that file. Then un-zip the file into the "EFI" folder.

Step 2
Configure MegaTune to 'see' the MSnSE software.

1) Open the MSnSE folder in "EFI" and run the "copyini" application. Once the file has been copied close the DOS window.

2) Then run the "edit-settings" application and make the following changes
i) Change the line "#unset MSNS_EXTRA" to # set MSNS_EXTRA" by highlighting the "un" and changing it to a double space.
ii) Change the default "# set MSI" (or whatever it is )to "#unset MSI"
iii) Click on 'File' then 'Save'
iv) Then close the Notepad window.

Step 3
Download the MSnSE file to your ECU (You WILL need to have the laptop connected to the Megasquirt for this to happen).

Now this can happen in two different ways depending on what temperature sensors you are using.

1) GM IAT and GM CLT

Run the "download-firmware' application from the MSnSE folder in "EFI"

i) Select the COM port to match your laptop (it is usually COM 1)
ii) Type 'Y' to answer the upgrading question
iii) Then follow the rest of the instructions BUT you don't need to install the Boot Jumper as the software will compensate for you.
iv) Once the firmware on the ECU has been wiped it will load the new code onto the ECU, this is currently about 1700 lines of code.
v) Close the application once the firmware has been downloaded
vi) Open up MegaTune, check that the commuincations is going through the same COM port as before, and if you see the guages in MegaTune giving some readings you can now download your .msq onto the ECU and you're good to go.

2) GM IAT and Mazda CLT

i) Once the laptop is connected to the ECU open EasyTherm
ii) Change the 'Code Version' (towards the bottom on the RHS of the screen) to "Custom"
iii) Change the port to your port (COM 1 or what-ever it is) on the bottom of the screen
iv) Change the 'Coolant Temp' settings to your desired settings ***(see below for the settings most people use)
v) Once you have changed the settings, click on the "Write .inc and .s19 Files" button on the bottom of the EasyTherm screen
vi) The file that you want to write to is the 'msns-extra.s19' file in the "EFI" folder in the MSnSE file that you unzipped to earlier.
vii) Then click on the "Download to Megasquirt" button on the bottom of the EasyTherm screen. This will open the file that you wrote to before, BUT it will default to the 'msns-extra.s19' file. You NEED to download the 'msns-extra.s19_mod' file. Don't do the other file!!!!
viii) Follow the instructions in EasyTherm to do the download BUT you don't] need to install the Boot Jumper.
ix) Once this has finished you will need to copy the "airdenfactor.inc", the "matfactor.inc" and the "thermfactor.inc" files from Program Files > EasyTherm into Program Files > Megasquirt > MegaTune2.25 > mtCfg
x) Then once that is all done, open MegaTune, check that the commuincations is going through the same COM port as before, and if you see the guages in MegaTune giving some readings you can now download your .msq onto the ECU and you're good to go.

*** The CLT settings that most people seem to use for EasyTherm are

-4F 16200
68F 2450
176F 320

I have found these figures to give a 'low' temp reading so I changed them a little to

-4F 16200
86F 2450
176F 384

This guide should be able to get your software up and running for MSnSE. I have personally followed the steps outlined above a number of times for software changes that started out at 024s9, then went through all of the upgrades to 029l, then the special ignition idle control version of the software, then the Hi-Res versions of the software and now back to 029v. However, I do not guarantee that you will have the same success as I have had using these steps so I will give the usual disclaimer that you follow these steps on your own choosing and I am not responsible for any stuff ups that may happen for your install.