The 1099-B proceeds should be showing the cash and fair value of Takeda shares received on January 8, 2019. The cost basis on the 1099-B should be the cost basis of your Shire shares exchanged. It is straightforward. I would call Schwab up and ask them to explain how the basis is zero. Also, the Takeda shares received should have a cost basis of the fair value ($19.025 per shr) on January 8, 2019, which is also used as a component of proceeds.
Summary of 1099-B details:
Proceeds = Cash rec'd ($90.99 per Shire Shr) + Number of Takeda Shrs rec'd x FMV price $19.025
Note: you received 5.034 Takeda shrs per 1 shr Shire
Cost Basis = Cost basis of Shire shares (look at your Dec 2018 Brokerage Statement)
Gain or (loss) = Proceeds less Cost Basis
