I found the exact same problem posted on xda developers fourm but none of the posts were answered completely or solved.
I rooted my Sm n900 without any problems, installed CWM recovery, installed SuperSu and installed VN Rom for galaxy note 3 (referred this from some Chinese guy on web (since i cant post third party links) its galaxynote3root dot com.
At first i didnt check efs backup option and installed VN rom without any problems (no imei loss or baseband unknown) on my own phone.
But when rooted one of my friends SM n900 with exact same method as i did earlier (but i checked create efs backup this time), i got screwed.
I tried EFS professional, but when i try to put his phone in RMNET + DM + MODEM by pressing *#0808#, and run efs software, and click either qualcommn or efs professional button, it doesnt recognise the device and says not connected.
I tried various other options as well such as rerooting, reinstalling the rom, reinstalling OEM rom, and other roms as well. Every thing is fin except IMEI and baseband null/unknown.