When the San Francisco 49ers signed both general manager John Lynch and head coach Kyle Shanahan to six-year contracts, the Niners’ front office knew the team’s rebuild would be a multi-year process. In the two years under the new regime, each of the 49ers’ personnel moves in free agency, and the draft was made with an eye toward the future. With San Francisco primed to enter the third year of their rebuild, “the future” is about to arrive, and results are expected to follow.

Lynch and Shanahan have put the 49ers in a position for success, despite the rocky nature of their first two seasons in San Francisco. The first-time general manager and head coach began their tenure with nine consecutive losses but set an NFL record by losing five straight games by no more than three points.

From a Pythagorean expectation perspective, the 49ers’ close losses were a good thing. San Francisco remained competitive during their string of losses, and given the fact that NFL teams win roughly half of their one-score games, the 49ers were likely a better team than their record indicated. But the Niners soon broke their close-game losing streak with a pair of blowout losses, including their biggest defeat in Levi’s Stadium history.

Jimmy Garoppolo, 49ers

So, back to square one of the rebuild. Perhaps the San Francisco 49ers were a bad team. But the stars soon aligned for Lynch and Shanahan, as the Niners acquired quarterback Jimmy Garoppolo from the New England Patriots amidst the strangest of circumstances. The future was suddenly bright for the 49ers as they ended the 2017 season with a five-game winning streak and a new franchise QB.

Unfortunately, the 2018 season has failed to meet the team’s lofty preseason expectations, as the 49ers lost their new starting quarterback to injury in Week 3. San Francisco quickly fell back into their trend of losing close games, but with the pending return of Garoppolo and other injured starters, the 49ers expect to contend in 2019. Over nearly two seasons, Lynch and Shanahan have built a strong nucleus of players, but the Niners still lack a few key pieces. With roughly $70 million to spend, the team will be active in free agency in 2019 — and the San Francisco 49ers’ sights should be set on the following three free agents.

49ers Free Agent Target No 3: EDGE Dee Ford

Despite drafting a defensive end in the first round of three consecutive drafts, the San Francisco 49ers biggest need remains at the EDGE position. The Niners’ most recent attempt at addressing this deficiency was also Lynch’s first draft pick as an NFL general manager.

John Lynch

Lynch selected Stanford Cardinal defensive end Solomon Thomas with the third overall pick of the 2017 NFL Draft. Unfortunately, Thomas has proven to be more effective in the run game than the passing game, as the second-year player lacks the bend necessary to rush the passer from the outside effectively. After multiple position changes, Thomas may have found his home as a run-stopping defensive end on base downs and an inside rusher on obvious passing downs.

When the 49ers drafted Thomas, they expected the college star to be a three-down edge rusher, and a complimentary piece to defensive linemen DeForest Buckner and Arik Armstead. Instead, Thomas has been relegated to more of a rotational role and has amassed just four sacks over his first two seasons in the league.

Acquiring a premier edge rusher via free agency is an expensive proposition, but the 2019 free-agent market has the potential to contain an abnormally strong EDGE class, including two of Pro Football Focus’ three top edge rushers, Brandon Graham and Trey Flowers. If both defensive linemen — who excel against the run and the pass — hit free agency, pass-rushing specialist Dee Ford from the Kansas City Chiefs could be an interesting option for San Francisco. Although Ford’s career has been sidetracked by injuries, he racked up double-digit sacks in 2016 and has become perhaps the NFL’s top pass-rusher in 2018, as he ranks at the top of the league in both sacks and quarterback pressures.

Kyle Shanahan, 49ers

49ers Free Agent Target No 2: WR John Brown

Live and breathe the NFL?

🚨 Get viral NFL graphics, memes, rumors and trending news delivered right to your inbox with the Clutch Newsletter.

One of Lynch and Shanahan’s first moves of the 2017 offseason was the signing of nine-year veteran wide receiver Pierre Garcon. The 49ers needed a significant upgrade at the receiver position, and although Garcon wasn’t an elite talent, he was a tough wideout with excellent hands, and a player who led the league with 113 catches for Shanahan during their final season together with the Washington Redskins.

Garcon was everything the 49ers needed him to be over the first half of the 2017 season. The 31-year-old wide receiver demonstrated both a willingness to go over the middle and an ability to catch errant passes from a pair of subpar quarterbacks. Garcon led San Francisco with 40 receptions and 500 receiving yards over the first half of the year until a neck injury sidelined the wideout for the remainder of 2017.

Unfortunately, Garcon hasn’t been the same player since he returned to the field in 2018. Ongoing shoulder and knee injuries have affected Garcon’s ability to catch the football, as he’s fallen out of the ranks of the most sure-handed receivers in the NFL:

The San Francisco 49ers placed Garcon on the trade block last month, but although there was reported interest, nothing materialized. With only 286 receiving yards on the season, the wide receivers’ time in San Francisco will likely come to an end before he sees his scheduled salary increase in 2020.

While the 49ers expect rookie Dante Pettis to develop into a productive wideout, John Brown — who currently leads the Baltimore Ravens with 601 receiving yards and four touchdowns — would be an immediate solution at the position. After signing a one-year, $5 million deal with the Ravens, Brown could be available at somewhat of a discount, particularly if his statistics are adversely impacted by a long-term quarterback change in Baltimore. At 5-foot-10 and 180 pounds, the speedster certainly fits Shanahan’s receiver mold and could be the explosive playmaker the 49ers need in 2019.

49ers Free Agent Target No 1: FS Earl Thomas

When Shanahan left Atlanta for San Francisco, he brought Falcons head coach Dan Quinn’s defensive system with him to the Bay. Quinn’s version of the Cover 3 wasn’t his own — it was a system made famous by Seattle Seahawks head coach Pete Carroll, who used portions of schemes he learned from a variety of sources, including the University of Arkansas’ Monte Kiffin and the San Francisco 49ers’ George Seifert.

Earl Thomas, Seahawks

Shanahan hired defensive coordinator Robert Saleh, who knew the system and watched it develop during his time with Carroll, Quinn and Gus Bradley. A year later, the 49ers added cornerback Richard Sherman, the outspoken leader and the face of Seattle’s “Legion of Boom.”

The 49ers’ transition to their new defensive scheme has continued to be a work in progress. While the team’s lack of pass rush has played a role, the one important piece that San Francisco’s secondary lacks are the “Earl Thomas” single-high safety — a savvy playmaker with speed necessary to cover the deep middle of the field while protecting the sidelines when necessary.

San Francisco started the 2017 season with former first-round defensive back Jimmie Ward in this crucial position — until injuries forced seventh-round rookie Adrian Colbert into the starting role. The 49ers thought Colbert would become the team’s long-term solution at free safety until poor play and an ankle injury forced him from action earlier this season. Now, Saleh is forced to alternate between Ward and rookie defensive back D.J. Reed, depending on Ward’s weekly injury status.

If the San Francisco 49ers want the “Earl Thomas” safety integral to their defensive system, they can have him once free agency begins in 2019. Thomas will make a quick exit from Seattle after this season, and he should be fully recovered from his October leg injury in time to sign a lucrative long-term deal. Thomas’ services won’t come at a discount, but the 49ers will have the rare opportunity to land the prototypical centerpiece to their defense — and perhaps the missing piece for a potential playoff run in 2019.