Just follow this method,
http://forum.gsmhosting.com/vbb/13285088-post40.html create your security area / partition backup,
Then erase eMMC, write full firmware released by any date, that's not a big matter.
Just Write by Samsung Vendor full firmware PIT, BL, AP, CP, CSC files, restore security backup data, your IMEI and network will be restored without any problems.
Your phone will be OK with Download mode, when you remove the JIG connection soldering wire, must remove that's wire very carefully, especially CLK wire connection it's very sensitive.
If there is something wrong with the short circuit "CLK", Your phone can not come in download mode, but with all the information shown by JTAG device when you did direct ISP connection with eMMC.
Test by me !!!