I wouldn't worry too much, the F-5E has a lot of advantages on it's side. Superb maneuverability and the ability to carry missiles with little negative impact on that maneuverability are huge advantages. The MiG-21 may be able to carry more missiles but with the full 6 loaded it flies like a bus!
As for the R-3R, it is definitely in the time frame of these two jets, but given the F-5E's good RWR and the R-3's terrible turn rate I'm not too worried.
In the merge another boon for the Tiger II is that it actually has a decent gun-sight intended for dogfighting rather than shooting down bombers. If you've flown the '21 you'll know how crap that things sight is, it seems most people just use the fixed net.