In the real world, that would rarely happen. In any case, man to man comparisons are meaningless if those men don't get along well as part of a team. 
Matchfixing and infighting are very convenient excuses used by most Pakistani fans to brush over the fact that these guys were highly inconsistent and mentally weak under pressure. It's utter lunacy to think all high profile Pakistani defeats in the 90s were down to matchfixing.
		
		
	 
It’s a hypothetical though. We see all-time XIs being made all the time, with Bradman sitting next to Ponting and Tendulkar even though these men do not know each other. Put Vaas in the same team as Akram in ‘92, before he learned English, and they will fail to communicate effectively about the batsman’s weaknesses. 
Further, generally speaking, we always consider players at their peaks when doing such comparisons - when I list Waqar Younis in a team, I am not referring to the Waqar of 2003. 
Similarly, we consider the team at peak unity within the team, comradery, and with everyone giving in their 100%. If we are not, then I am on the same side as you — the team would lose, simply because it relies on the weight of individual performances while Virat’s unit works as a unit, and while some of those individual performances come under the scanner. 
However, that changes the entire gist of the thread. It is no longer “would Virat’s India have beat Pakistan’s 90’s team” but rather “would Virat’s India have beat Pakistan’s 90’s team including the possibility that Wasim Akram feigns injury one day into the match with varying reports of multiple men up to replace him as captain.”
I doubt anyone sides with Pakistan in that narrative. Instead, my comparison is with the imaginary 90’s team that always performed to the best of its ability and gelled as a unit.
I don’t think infighting is a convenient excuse for Pakistani fans, but rather a very inconvenient one because it opens a Pandora’s box of what-ifs which can be very painful to contemplate.
Not all high profile defeats in the 90s were down to match fixing, but it is likely that many were. I don’t think it’s fair to entertain any other possibility.
There is no comparison where Virat’s India stands a chance against that team, which goes toe to toe with 00’s Australia and 80’s Windies.
Lastly, a Test team’s overseas record always tells us more than its home record (a 50/50 record home and away is better than an 80/20 and a 20/80 split home and away).