It’s the behemoth flagship fund with a 17-year track record from a manager dubbed the bond king. But Pimco Total Return enters the final quarter of 2014 under a cloud of uncertainty.

For investors in the bond mutual fund. it means coming to grips with the abrupt Sept. 26 resignation of Pimco co-founder Bill Gross. And the significant outflow from PTTAX after his departure. And the three new faces at the helm, managing $221.6 billion in assets. And a ratings downgrade for the fund from a prominent investment research firm.

An investor may be tempted to bail out, but not so fast, say some experts. Despite recent stumbles, PTTAX’s longer-term returns and its new managers rank among the industry’s best, they note. Though new at the fund’s helm, they are not new to the fund or its investment process.

It is well-positioned to weather a pretty large storm, Eric Jacobson, a senior analyst at Morningstar Inc. wrote in a recent research note. At the same time, the firm lowered PTTAX to a bronze rank Monday citing the billions in outflow and management changes within the past week.

For jittery PTTAX-owning investors, alternatives abound. The most obvious involves its Core Bond peers such as $29 billion Dodge & Cox Income Fund or $18 billion Vanguard Intermediate Term Investment Grade .

Both funds have multisector allocations, similar to PTTAX. DODIX and VFICX are each up 4.5% year to date vs. PTTAX’s 3% gain. Their expense ratios are far lower than the Pimco bond fund’s 0.85%.

Look At Holdings

But when comparing options, investors should scrutinize the underlying holdings. The similar-sounding DoubleLine Total Return. while an excellent fund, offers greater exposure to the mortgage subsector than PTTAX, which allocates 20% to mortgages, said Todd Rosenbluth, director of fund research at S&P Capital IQ.

Make sure you’re looking at the funds in a largely apples-to-apples comparison to get the sought-after diversification, he advised.

Another straightforward alternative: a comparable ETF such as iShares Core U.S. Aggregate Bond (ARCA:AGG ). It tracks the same index as PTTAX, but offers greater transparency, tradability and a far lower expense ratio 0.08%. AGG has risen 4% so far in 2014.

Still, as a passively managed vehicle, it won’t outperform the market. That’s something that investors exiting the actively managed PTTAX and its ETF version Pimco Total Return ETF (ARCA:BOND ) are likely looking for, noted Rosenbluth.

To possibly achieve market-beating returns, he suggests using a bucket of ETFs to replicate the strategy of PTTAX, which has 41% in government securities, 20% in mortgages, 13% in U.S. credit, 13% in foreign developed markets and 9% in emerging markets.

The Weights

For government exposure, an option would be iShares 3-7 Year Treasury (ARCA:IEI ); for mortgages, Vanguard Mortgage Backed Securities Index (NASDAQ:VMBS ); and for U.S. corporates, iShares iBoxx Investment Grade Corporate (ARCA:LQD ).

You could take the top-down views that come out of Pimco and re-create some of it yourself, he said, adding this is a harder option requiring some investing expertise.

Investors considering a fund switch would do well to consult with their financial adviser, said Margo Cook, head of investment services for Nuveen Investments, which manages $231 billion in assets. Go to the ETFs page at investors.com to see Cook’s three points to consider before jumping ship.