Personally I will be surprised if, even ten years on, a small team with a limited budget will be able to enhance an F1 car constructed with a budget running into the multi millions and a couple of hundred strong team
Can't really argue with that... even if you have the skills/facilities/resources to even make the shapes that the 2007-2008 cars have adorning their bodies, without CFD or wind tunnel time how do you know what shapes to make to actually provide a benefit? That's why you can't really do flip-ups/turning vanes, etc that some people have suggested...
However remember that the Benetton F1 team in 1999 were working to a specific set of rules, and without these rules it should be possible to apply some generalised aerodynamic principles to (Hopefully!) improve things... without CFD and/or wind tunnel you won't know for sure until the mods are tried on the car though...
Some of the things already mentioned should bring improvements, if resources allow:-
Lowering the front wing (but ensuring you don't block off air flow when the car is pitching or under full aero load!)
Changing the diffuser design (steeper/longer -yes this might change the balance, but assuming you can change the front wing flap angle then you should(!) be able to get the balance back).
Widening the front and rear wings... in order to maintain the same level of downforce you can make the chord shorter... wide wings with short chords are supposedly more efficient, so for the same downforce you'd get less drag).
Increasing the height and length of wing end plates should (I say it again!) improve the efficiency of the wing, thus a lower angle is needed for the same downforce, therefore producing less drag)
Reduce the size of any wing mirrors (but still maintaing good rear visibility!)
Change the suspension arms so they have a more aerodynamic section
Remove any camera pods, if fitted!
The above list were all items constrained by the rules in 1999, and I imagaine are all "bolt-on" components, so could be changed at the track if the mods were found not be of benefit.....