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Ok, well since you are having issues with hyperterminal, you can use a program called, EasyTherm. Its a bit easier to use. Download it here:
http://www.megamanual.com/EasyTherm_Full_Install.zip
Once you get easytherm loaded, you are ready to load up the .s19 code file from the 029q2 unzipped files folder. BE SURE YOU KNOW YOUR COM PORT YOU ARE USING!! You MUST know the com port number when connecting your MS to the computer, and this software program needs to know this as well.
1. Open Easytherm
2. At the bottom of the easytherm window, you will see the drop down for the correct com port, so select your com port number
3. Slightly up and to the right side of the window, you will see "code version", and from here you select, "custom"
4. Now, power up your MS, WITH THE BOOT LOADER PINS SHORTED TOGETHER, OR USING A SWITCH, whatever you have done in order to get into boot mode.
5. Now hit the button at the bottom of the window, "download to megasquirt", and a screen pops up, which is where you will need to find the 029q2 .s19 file. Once you find the .s19 file, open it, and it will take it from there. Just follow the onscreen messages. It does take several minutes for the upload to complete, so be patient.
once its all done, turn off power to the MS, and dissconnect/turn switch off from the "boot" loader pins on the MS board.
Now in order for Megatune to read this new code, the proper configuration file(extra.ini) needs to be in your car project folder, the one MT will be reading when you open MT.
Its easy to use the "megatune Configurator" program to help with this a bit. If you dont have it, download it and use it!
1. Open MT configurator program
2. At the top, click "project", then "new"
3. Name your new project to whatever you want, anything other than "car 1"
4. Now your new project will show on the left side there, with the plus signs next to it. Click the plus sign next to your project you just named.
5. click the "settings.ini" plus sign
6. Now you will see "settings", and on the right side of your screen, will be all the variants you need to configure.
7. Click on the first thing you see on the left under the settings, which will be, "code variant". You will notice that on the very top of the screen will be a white window, with a drop down at the very rightmost part of the screen. Hit the drop down, and select" msns extra".
8. Next, click on "idle controller" from the left side again, just like the last time. Again, go to the topmost dropdown to select what you want. The first setting is fine for idle controller.
9. "lamda sensor" - If you are using a wideband, see if its in the list there, and select it.
10. "lamda" - leave alone
11. fueling algorithm - leave alone
12. Pretty much everything else should remain at the default values, except your map sensor type, assuming you UPGRADED with a map sensor, OTHER than what was supplied in the kit. The supplied map is a 2.5 bar. Its the MPX4250, 250 kpa sensor.
13. When you are done, go to "file", then hit "save". Exit the configurator.
Now for that .ini file. Go to your 029q2 unzipped folder with all of the 029q2 files in it, and find the " msns-extra.ini" file. It should be 181kb in size. Right click over that file, and hit "copy". Now you need to go to the megatune directory file in the Megatune program file directory.
1. Right click "start" from windows, then hit " explore"
Go to C drive, "program files", then "megasquirt"
2. depending on how you have this setup, you should see a folder somewhere named, "Megatune 2.25" with a plus sign next to it. Hit the plus sign
3. You will see a folder, "mtCfg" then just click on it to view the folder contents. THIS IS WHERE YOU WANT TO PUT THE "EXTRA.INI" FILE! If you right clicked and copied it correctly from earlier, right click again, and hit "paste". A warning will come up, and you want to REPLACE THE FILE with your new one you are putting in there. Thats it!
Close it all out, and open up Megatune. You will see a small screen come up, and select your project name. MT will come up, and it should be reading your MS properly when its powered up.
I took you through the manual way to copy the .ini file to the megatune directory, as i have had issues with the "copy ini.bat" file not doing the job correctly. This way, you know the file is in the proper directory. If it still doesnt work, then either you did something wrong, or somethign with the MS isnt right.. 
13.5 @108 MPH-2.2 60ft(stupid FWD!)
S16G @ 18 PSI/FMIC/Running on MegaSquirt II (Now with sequential
fuel injection)
My webpage: http://eclipsed4evr.home.comcast.net
-1998 Mitsubishi Eclipse RS-T- "Toy"
-1992 Plymouth Laser Turbo AWD(SOLD)
-2000 Honda CR-V(daily)
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Are you waiting long enough for the code to upload to the processor? Is it saying its successful? Are you sure you are shorting the 2 "boot" sections on the board correctly when uploading? Are you powering up the MS while downloading? Are you dissconnecting the boost pins afterward? Almost sounds like the code isnt getting programmed correctly. Are you using a serial port on your computer to upload, or a USB Adaptor? It looks like you are getting the ini file in the correct directory, because the warning message you are getting is saying that MT is expecting 029q2, but its not getting that from the processor. So i think thats fine. It sounds like the code is not either getting programmed right, or not getting programmed at all to the processor. Use a straight serial connection on a desktop computer if you have it, and try again. If it still does not work, then you may have a corrupt bootloader section in your processor. A new processor would be in order to correct that. The bootloader section is not erasable as far as I know, so i dont know. I know others have had issues trying to load code when using a serial to USB adaptor, so use a desktop computer with a serial port to load the code, if you havent tried that already.