SANTA CLARA, Calif. — When Raheem Morris accepted the San Francisco 49ers’ defensive coordinator job this past winter — becoming the fifth coordinator in five years in Santa Clara — he knew he had his work cut out for him.

There’s just no way he expected he’d have this much work to do.

On Wednesday, the 49ers are boarding a 16-hour flight across the Pacific to play a real football game in Australia — super normal, right? — but even after months of planning, development and preparation, the Niners’ defensive coordinator will be packing a duffel bag full of questions.

Sure, the Niners have Fred Warner, Deommodore Lenoir and other standouts who will be counted upon come Game No. 1 and beyond.

But when it comes to the pass rush, a starting defensive tackle, a strong-side linebacker and a field-side cornerback, the Niners will arrive in Melbourne on the clock — time-zone change be damned — to find answers.

Putting together a defense, on a tight deadline, 7,500 miles from home? What could go wrong?

The most glaring of the issues for last year’s defense:

The pass rush. Or lack thereof.

The Niners had a measly 20 sacks last season, six fewer than the second-worst team in the NFL, the Jets.

Yes, the kids would say that the Jets were “sackmogging” the Niners last year. You don’t emotionally recover from something like that.

Mere hours before wheels up for Melbourne, San Francisco doesn’t have a single fully healthy edge rusher ready to pin his ears back and attack Matthew Stafford Down Under.

Nick Bosa practiced on Wednesday — the Niners’ last practice stateside before the Week 1 game — but that gives him a mere week before he has to play a divisional game.

Seeing as he hasn’t played 11-on-11 since Week 3 of last season, is that enough ramp-up time?

We saw something similar to this after his 2023 contract holdout.

He didn’t practice with the team all spring and summer, strolled in just before Week 1, and spent two months playing like he had sandbags tied to his cleats.

Now, fresh off another vanished training camp, the Niners expect him to hop off a transpacific flight and immediately terrorize an NFL backfield.

Oh, but this time he has a surgically repaired knee that’s acting balky.

Still, Bosa is the load-bearing wall of this pass rush.

If Bosa doesn’t look like the player the Niners presumed he would be this season — and that’s hardly a dubious presumption — who’s getting after the quarterback?

The gate agent at the airport?

Behind Bosa on the depth chart, the pass-rusher cupboard remains rather bare.

Sure, they drafted Romello Height in the third round this past April, and he has shown impressive flashes in camp, but he’s a situational pass rusher at best at this early point in his career and, whoops, he’s also injured.

Perhaps the pass rush can come from the interior. Offseason acquisition Osa Odighizuwa has been magnificent — powerful and lightning-quick — in camp and looks poised to be the gap-shooting defensive tackle this team has sought since D.J. Jones left for the Denver Broncos in free agency before the 2022 season.

But to do that, Odighizuwa needs the defensive tackle next to him to draw some attention.

And training camp and preseason action have not produced that reliable gap-filler. Alfred Collins is still a theory, C.J. West had an up-and-down August, and the best option might be an undrafted free agent, James Thompson. Selecting a starter among the three of them will likely go down to the wire.

Then you look at the second level, and the questions continue.

Morris has spent the last few months preparing the Niners to play a different kind of defense, one that utilizes a strong-side linebacker as a jack-of-all-trades “star” player, along the lines of Budda Baker in Arizona, Derwin James for the Chargers and Niners foil Nick Emmanwori in Seattle.

But if the Niners have a player of that ilk, he has not shown himself yet.

Special teams ace and last year’s SAM linebacker (to disastrous results from scrimmage) Luke Gifford hasn’t practiced in weeks. Meanwhile, rookie Jaden Dugger is being asked to play an exotic hybrid position, and he currently looks like a tourist trying to understand the Melbourne train system.

Morris felt it important Tuesday to remind reporters that Dugger is a rookie.

“We see the super highs,” Morris said. “Then he showed a couple lows in the box and being able to be confused, things of that nature. But you see the splash plays, you see the length, you see the talent and he’s exciting … I think the whole goal for me and the whole goal for Dugger is just to get better throughout the course of the season and to be ready whenever his number’s called.”

That’s classic coach-speak for: We threw the kid into the deep end, and we’re surprised he’s swallowing pool water.

And also, don’t expect that number to be called anytime soon.

Because Sean McVay is watching that preseason tape and practically begging the rookie to be out there.

So much for that “star” player idea.

Then there’s the back end, Morris’ bailiwick.

Morris wants to run Cover 6, an intricate split-safety look that asks defensive backs to be part-time safeties and full-time mind readers.

The entire engine runs through an “apex” defender, the corner who ties the outside flat to the deep seam.

That linchpin was supposed to be Renardo Green.

It might still be him, but he has been battling a hamstring injury since the Niners’ second preseason game, robbing him and the Niners of vital practice time the past two weeks. While Green had shown strides since the end of last season — when he was publicly reprimanded on the sideline by Kyle Shanahan for messing up a Cover-6 play in the playoff win over the Eagles — he was still a work in progress.

Trying to run Cover 6 without a top-tier field-side corner is like trying to make an omelet without eggs.

If Green can’t go, or is simply ineffective against a Rams offense that led the NFL in points per game last season, it’ll be the mercurial and buccaneering Jack Jones playing a role that asks for consistency and steadiness.

What could go wrong?

Morris has a Super Bowl ring, a booming laugh and enough charisma to charm the stripes off a tiger.

But every ounce of his reputation as a defensive pragmatist is being put to the test in these final days before games start.

Yes, Morris has his work cut out for him, but at least he gets 16 quiet hours in business class to draw up a solution — if one is to be found.

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