1986 Mets vs. 1998 Yankees: Who Would Win?

This question was asked on Quora: If the 1986 Mets played the 1998 New York Yankees, who wins?

"Curious who would win an epic clash of two of the most dominant baseball teams of the modern era.  Assume a seven-game series.  Four at old Yankee Stadium; three at Shea (Yanks has 114 wins, Mets 108).  Who wins, and why?"
Here's my answer, in full. I've reprinted it here, with some editing:
This is a joke. The '86 Mets were 1 Astro run away from facing Mike Scott in Game 7 in the Astrodome and missing the World Series completely. The Mets have won 2 World Series, but the wrong one is being called a "miracle."

Let's look at it using the actual pitching assignments from the World Series in question, the Mets in 1986 and the Yankees in 1998. I'll even give the Mets the home-field advantage, because the '98 Yanks wouldn't care, having gone 6-1 on the road that postseason.
Game 1 at Shea Stadium: Ron Darling vs. David Wells. An effective lefthanded pitcher shuts down Keith Hernandez and Len Dykstra, and, if Mookie Wilson plays, forced him to switch to his considerably less effective right side.
In the actual 1998 WS Game 1, Wells was a bit shaky, allowing 2 runs in the 3rd inning and 3 in the 5th, before the Yankee bats bailed him out with 7 in the 7th. But in 1986 WS Game 1, the Mets faced a lefty, Bruce Hurst, and got just 4 hits all night.
(Remember, the Mets lost the 1st 2 games at home. I still remember the Daily News headline after they lost Game 2 to the team from Beantown: "BEANS!")
Yankees lead, 1 game to 0.
Game 2 at Shea: Dwight Gooden vs. Orlando "El Duque" Hernandez. El Duque won his 1st 8 postseason decisions. Ironically, it was the 2000 Mets who ended the streak. But the 1986 Mets? They'd never faced anything like El Duque before. (At the time, no one in North America had.) In Game 2, they got 3 runs on 8 hits off Roger Clemens, Steve Crawford and Bob Stanley. On this night, they'd be facing a likely combination of El Duque, Mike Stanton and Mariano Rivera.
The Yankees, meanwhile, in their Game 2, scored 6 runs in the 1st 2 innings and never looked back. What's that, you say, the Mets have Dwight Gooden? Guess what: Gooden pitched in 2 games in the '86 WS, and didn't win either one. He allowed 6 runs in 5 innings in Game 2, and lost Game 5 as well.
Yankees lead, 2 games to 0.
Game 3 at Yankee Stadium: Bob Ojeda vs. David Cone. (Remember: The Mets didn't get Cone until the next year, reaching the Playoffs with him in 1988, but no Pennant; while the Yankees won 4 World Series with him.) The trade of Calvin Schiraldi to the Red Sox for Ojeda essentially decided the '86 WS.
The "conventional wisdom" is that you don't start a lefty at Fenway Park, because of the Green Monster. Well, the '78 Yankees with Ron Guidry and the '86 Mets with Ojeda proved that the conventional wisdom wasn't very wise. But Yankee Stadium was a better park for a lefty pitcher because it's a bad one for righthanded hitters. Ojeda pitched very well in his Game 3, and the conditions will be easier for him in this simulation.
In contrast, Cone ran out of gas in the 6th in 1998 WS Game 3, and might do so sooner this time, because the Mets scored 4 runs in the 1st in 1986 WS Game 3.
Mets close to within 2 games to 1.
Game 4 at YS: Darling or Sid Fernandez vs. Andy Pettitte. Darling pitched very well on 3 days' rest in his Game 4, but Pettitte was better in his, taking a shutout into the 8th inning, and it was preserved by Jeff Nelson and Mariano Rivera. This is where the Yankees' better bullpen really comes into play.
The Mets scored 4 runs in the 3rd in their Game 4, but Pettitte is a lefty, so, again, it will be considerably harder for Hernandez, Dykstra, and Mookie. (Since there will be a DH in the YS games, both Nails and Mookie will be playing.) Pettitte might bend in the 4th, but he won't break. If he does, Joe Torre has options, with Graeme Lloyd and Ramiro Mendoza, both of whom pitched less than an inning in 1998 WS Game 3 and, even if they did so in this Game 3, would still be ready to go.
In contrast, if the Yankees threaten Darling (who, remember, is pitching on 3 days' rest), who does Davey Johnson have to come in and put out the fire? Rick Aguilera, Doug Sisk, Roger McDowell? It's way too early to bring in your closer, Jesse Orosco. (Unless you're Billy Martin and you've got Sparky Lyle: See 1977 ALCS Game 4. Dick Williams also did that with Rollie Fingers on the 1970s A's.)

What Johnson could do is bring in Sid Fernandez. Better yet, he could go to a 4-man rotation and start the lefty El Sid, who was brilliant in that Series, allowing just 1 run in 6 2/3 innings, all in relief, including the last 4 innings of Game 5 in the little green pinball machine off Kenmore Square. If Sid starts, the Mets have a better chance.
Which doesn't necessarily mean they would win. In 1986 WS Game 4, the Mets scored 2 in the 7th and another in the 8th, but in the 7th and 8th innings of this Game 5, Torre would not have Crawford and Stanley pitching, he'd have Stanton and/or Nelson, and then Rivera for the 9th.
Yankees lead 3 games to 1.
Game 5 at YS: Gooden or (if Sid starts Game 4) Darling vs. Wells. Doctor K on 3 days' rest vs. Boomer on 4? Since the Yankees swept in '98, we have no record of how Wells would have pitched in a Game 5, but he had been lights-out in that postseason, making him 21-4 counting the regular season.
In contrast, we know how Gooden pitched in 1986 WS Game 5: He allowed 4 runs and didn't get out of the 5th inning. Whether he was secretly injured, or feeling the effects of cocaine, or simply letting the pressure get to him, we don't know. What we do know is that, contrary to what he looked like in 1984 and '85, he was not the greatest pitcher in the world that night in the Back Bay, and there's no reason to believe he would have been any better in the South Bronx against a team that was better than the '86 BoSox.
The big variable is if Johnson starts Sid in Game 4, pushing Darling to Game 5, and, if necessary, Doc to Game 6 and Ojeda to a deciding Game 7. But, again, there's the lefty factor. The Mets got just 2 runs on Hurst before, tiring on 3 days' rest, they got 1 on him in the 8th and another in the 9th, as John McNamara didn't trust his bullpen. Wells would have been a lefty on 4 days' rest, and with a much better bullpen.
Yankees win Series, 4 games to 1. The Mets win only Game 3 -- just like in the real-life 2000 WS.
There you have it, Met fans: It didn't even get to a Game 6. If it had, it would have been El Duque against either Ojeda on short rest or a pressure-wracked Doc. And there's still no Schiraldi or Stanley in the Yankee pen: There's Lloyd, Mendoza, Nelson, Stanton and Rivera. And Jorge Posada (a better catcher than Mike Piazza, and at least in Gary Carter's range defensively) to block any wild pitches, as opposed to Rich Gedman; and Tino Martinez to field grounders at 1st base and flip them to Rivera to cover the bag, unlike Bill Buckner and Bob Stanley.
If it still goes to a Game 7, it's Pettitte vs. Darling, who'd be exhausted, or Ojeda. But the number of things that would have had to go right for the Mets to even reach a Game 6 is staggering.
The '86 Mets wouldn't have beaten the '27, '36, '41, '53, '56, '61, '78 or 2009 Yankees, either.