2G/3G network needs proper settings. Wifi needs network in range. Do you have these two conditions fulfilled?

What's wrong with File manager and x-terminal? Describe it more.

App Manager is useless, if you don't have network. At this point you can only remove apps.

You described that you flashed device twice. Maybe you made something wrong already at this point? When flashing firmware (PR1.3) and eMMC together, firmware must be flashed first and after procedure is completed, then must be started eMMC flashing.

So, first do:
flasher-3.5.exe -F RX-51_2009SE_20.2010.36-2_PR_COMBINED_MR0_ARM.bin -f

and then
flasher-3.5.exe -F RX-51_2009SE_10.2010.13-2.VANILLA_PR_EMMC_MR0_ARM.bin -f -R

It's hard to help you, because we can't see you phone "in action". The best way to check things is, if you could find someone near you who has working phone and compare everything with him.