I don't think a forward swept wing was a very practical idea for an operational aircraft. So Berkut should be out. I'd be putting my additional development money on Yak-43 actually and the single engine Yak stealth follow on.
I left the SU-47 in order to change the least possible amount of things from TTL. If I had to choose a plan to modernise the airforce I would have kept updating the old Su-27 while putting into service the Sukhoi Su-37 "Flanker-F" around 2002 and start the PAK-FA project around 1999-2000. Thanks to more funding and a combined effort by both Sukhoi and MiG (from this the proposed name SM-57 instead of Su-57) the first prototype would be ready around 2006 and the aircraft could become operational as early as 2010, even if I think that 2012 is a more reasonable date.
Then I would focus on building a stealthy and supersonic successor to the Su-25 and MiG-27 ground-attack aircraft to enter service in the 2020-2022 period; something like the fictional Yakolev Yak-49: a single-seat, twin-engine, all-weather stealth attack aircraft, designed to perform ground attack, aerial reconnaissance, and, to a limited degree, air defence missions.
https://www.deviantart.com/sport16ing/art/Yak-49M-Buturlinovka-Air-Base-early-2016-795043124.
In the end, develop the PAK-DA and the MiG-41 and have them enter service in the late-2020s/early-2030s while upgrading the Tu-160 and Tu-22M fleets and slowly retiring the Tu-95s.
The Russians don't really need VTOL aircraft if they don't have helicopter carriers. Yes, they have two nuclear carriers but they will use only Su-33 and MiG-29K(simply to give a lifeline to MiG too, not to mention helping with exports) together with Ka-27 and several Ka-31 AEW helicopters.