I'm not really understanding what you've said in that first paragraph but I've addressed the Baxalta / Shire transaction here:
https://ttlc.intuit.com/questions/3814587-can-you-help-baxalta-shire-merger-cash-and-stock
The transaction is fully taxable and the "proceeds" of the sale is the sum of the cash received plus the FMV of the stock received. Your broker has simply broken the proceeds into two parts.
You need to go back through you records and determine your cost basis for the Baxalta stock you've tendered. That's your obligation as a taxpayer and investor. The you subtract that basis from ALL the proceeds. (There's really no need to report it as two sales.) And you have your resulting gain or loss.
Tom Young
