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A small microphone or "bug". The movie offers a small glimmer of hope that the investigation might continue, even after all the previous tragedy. However, given the scene in which the Ayala's lawyer says he sweeps his office for bugs twice a day, there is little chance that the microphone will be there long enough to gather any useful information. Edit
Helena's deal, which she did to secure her husband's release free of the charges against him, involved 3 parts:
The first part being the 3 million dollar debt her husband owes would be forgiven.
The second part of the deal is that Helena's husband would become the sole distributor for the cocaine that the Obregóns would ship over the border in the dolls. Such a move would serve to rebuild Carlos' failed business that was destroyed when Ruiz was busted. Carlos and his wife would become very rich again, as would the Obregóns.
The third part was that the Obregóns would agree to assassinate Eduardo Ruiz, the prime witness in the prosecution's case against Carlos.
In return for this she gives Obregón the formula and procedures for turning cocaine into bunny dolls that resemble high impact plastic. The cocaine would also carry no odor so that it would be undetectable by dogs used by the DEA border agents to find illegal shipments of drugs. When the dolls are placed in a solvent, the cocaine immediately dissolves and can be dried out and sold as powder. Because so many products like the bunnies are made and imported from Mexico (and other countries), shipping drugs across the border would be very easy for the Obregón cartel. Edit
Played by Dennis Quaid, Metzger was Ayala's power of attorney. When Ayala was arrested he could no longer make any business decisions and that responsibility transferred over to Metzger, who was fully aware of Ayala's involvement in drug trafficking and had all the info regarding his estate and finances.
At first, Metzger appears to be practicing due diligence as a power of attorney, but it is eventually suspected by Ayala that he's trying to take over his empire by withholding the means and money to pay off the Obregons. He's also suspected of setting up Ruiz' as he was Ayala's main supplier to the US, thus leading to Ayala's arrest when Ruiz implicated him. Lastly, it's hinted that Metzger also had affections for Ayala's wife.
This was all culminated in the final phone call between Ayala and Metzger where Ayala accuses him of the above after he was acquitted (due to Helena's deal with the Obregons, after Ayala surrepticiously told her where the blueprints for the doll distribution were hidden in the picture on the wall of their home). We then see two hitmen enter Metzger's office with guns in hand ready to eliminate him. Edit
It isn't answered explicitly, but the most logical reason is to use the vehicle to extract the witness to a safe location. Since Ray Castro, in the heat of the moment, was focused on the foiled assassination attempt right in front of him, it wasn't an unreasonable course of action even if it ultimately led to his own demise. Edit