Explanation
The alert that the network engineer should configure based on the operation specifications is SNMP traps to report when the chassis temperature exceeds 95°F (35°C). SNMP (Simple Network Management Protocol) is a protocol that allows network devices to communicate their status and performance information to a central management system, called an SNMP manager. SNMP traps are messages that are sent by network devices to notify the SNMP manager of an event or condition that requires attention, such as an error, a failure, or a threshold violation. In this case, the network engineer should configure SNMP traps on the network devices to send an alert when their chassis temperature exceeds 95°F (35°C), which is the maximum operating temperature specified in the table. This alert would help the network engineer monitor and troubleshoot any overheating issues that could affect the network performance or availability. References: CompTIA Network+ N10-008 Certification Study Guide, page 228; The Official CompTIA Network+ Student Guide (Exam N10-008), page 8-11.

The application layer is the highest layer of the OSI model, and it provides the interface between the user and the network. It does not handle the details of packet delivery, such as addressing, routing, error checking, or encryption. Those functions are performed by the lower layers of the OSI model. The application layer only focuses on the format, content, and presentation of the data.
Reference:
Understanding the OSI Model - N10-008 CompTIA Network+ : 1.11
CompTIA Network+ Certification Exam Objectives, page 92

The most likely cause of the issue where the fiber connection from a device to a switch is not working is that the TX/RX (transmit/receive) is reversed. When connecting fiber optic cables, it is important to ensure that the TX of one device is connected to the RX of the other device and vice versa. If the TX/RX is reversed, data cannot be transmitted successfully.
Reference:
CompTIA Network+ Certification Study Guide, Exam N10-007, Fourth Edition, Chapter 5: Network Operations, Objective 5.1: Given a scenario, use appropriate documentation and diagrams to manage the network.

Explanation
iperf is a tool that can measure the bandwidth and quality of a network link by generating and transferring TCP or UDP data streams. iperf can report the maximum achievable throughput, packet loss, jitter, and other statistics for a given link. iperf can be used to test both the uplink and downlink performance of a network link by running it on two endpoints and specifying the direction and duration of the test. iperf can help the engineer verify that the new fiber uplink meets the throughput requirements for the office network.
tcpdump is a tool that can capture and analyze network traffic by filtering and displaying packets based on various criteria. tcpdump can help the engineer troubleshoot network problems, monitor network activity, and inspect packet contents, but it cannot measure the throughput or quality of a network link.
ping is a tool that can test the reachability and latency of a network host by sending and receiving ICMP echo packets. ping can help the engineer check if the new fiber uplink is connected and responsive, and how long it takes for packets to travel between the endpoints, but it cannot measure the throughput or quality of a network link.
netstat is a tool that can display information about the network connections, routing tables, interfaces, and protocols on a network host. netstat can help the engineer view the status and details of the network connections using the new fiber uplink, but it cannot measure the throughput or quality of a network link.
References
iperf - The ultimate speed test tool for TCP, UDP and SCTP
How to use iperf to test local network LAN speed in Windows 10
How to Test Network Performance Between Two Linux Servers
What is tcpdump?
8 Common Network Utilities Explained
Monitoring Your Network: ping, netstat, tcpdump, and Ethereal
Netstat vs. Nmap vs. Netcat: Understanding the Differences