the firmware and Megatune version need to match dude.
What hardware are you running?? installed code varaint and firmware??
You want MT2.25 setup for msns-E ( open the car1 folder and check/tweak the MTCFG file with notepad and resave with the same filename
then try to connect again, it sounds like the ECU itself is on its default Ms1 setting with the OE MS1 firmware on there.
you'll need to download the MSnS-E firware to the unit, use the latest stable release, 029y4 I think , the you should be able to populate the tables and get started
Re the USB , yes its a PITA, and if you're using a stim and 9V batt to flash, you'll have real issues as the burn voltage is much higher than the PP9 can provide more than once.
the Baud rate is dependant on hardware Ms1 or 2
All good fun
