So I have a main account which is in no way linked to my second account which is where my botting takes place. Since both accounts are in my name, would transferring over a 90 from the botting account to the main account risk the main account?
Using the bot account from the same IP address as your main account is enough to link them, but blizzard generally only ban the offending account. They'll sometimes ban other accounts which have benefited from the botted account too, but that's less frequent it seems.
TL;DR - Anything related to botting can't be classed as 'safe'.
That is a little bit misleading.. for the record, even if you merged BOTH accounts to the same battle.net account, only the actual account that was in violation is ever banned, not any other account on the battle.net account, nor the battle.net account itself. This being said, it would be 100% safe to transfer your characters to and from the accounts and the main account would be safe as long as no botting happened on IT, even if both were merged and the other were banned.
blizz will ban whatever they want. period. they do not have to give a reason, there doesnt have to be any evidence. if you dont believe me, try to get an account unbanned by calling blizz. they will tell you this.