The problems began when I started a new character with an alternate start mod. For some reason general tullius did not spawn and Legate Rikka has been talking to a wall since i showed up in solitude.

IN order to join the legion, I had a to manually spawn general Tullius. I was able to swear the oath to him but he hasn't been engaging in the quest driven dialogue he has with Rikka. She still talks to the wall while he calmly sits somewhere else.

Now upon retrieving the Jagged crown, I can't return it to him as it's not in the dialog options. Is there a console command I could type that may get the clone general tullius back on track?

It sounds like the alternate start mod might have broken that particular quest chain. Even if you do progress past this point, it will likely cause further issues down the road.

However, if you feel like pressing on you can use the "SetStage" console command to manually move the quest forward.

http://elderscrolls.wikia.com/wiki/Console_Commands_%28Skyrim%29#SetStage_.3Cquest_id.3E_.3Cstage_value.3E

http://www.uesp.net/wiki/Skyrim:The_Jagged_Crown_%28Imperial%29#Quest_Stages