Maybe I'm missing the point entirely and maybe I should return to my box, but what do you mean by 1000-3000 lines?
When playing a 3DN system on 649, the base of your system should be a C(46,3,2,3) i.e. playing 46 numbers in a pick 3 system with a guarantee of 2 if 3 hit.
The whole point of having 3DN is that you assume that they will hit. You already have 3 numbers, so you need to play the remaining 46 numbers.
Since every line already has 3 DN's, you only need 3 more numbers on each line.
A full 46/3 system contains 15180 lines, which is a little too much, that's why we go for a guarantee of 2.
The hit is already 3 (if your DN's are picked correctly), so you only need 3 more.
So in fact, the C(46,3,2,3) is effectively transferred into a C(49,6,5,6) or, in other words, you'll have a 5 number hit IF your 3DN hit!
The C(46,3,2,3) can be done in 170 lines. Although I haven't got this wheel you should be able to do fine with CoverMaster to get an approx. 200 lines not-so-well-optimized equivalent.
A 2DN system is a little more expensive and does in fact enter the 1000+ regions. For a 6/49 2DN system, you should use C(47,4,3,4), which CAN be done in 1815 lines.
Super 7 is a little more expensive:
3DN: C(46,4,3,4): 1726 lines.
If you'll use the same strategy for a 2DN for Super 7, you'll find that it is too expensive: C(47,5,4,5) = 15205 lines.
A nice alternative is C(47,5,3,5) in 411 lines, given you a 5 (instead of a 6) number hit if your 2 DN's hit.
So, in the worst case scenario, you're looking at 1815 lines max, whereas the number of lines for 3DN in 649 or 2DN in Super7 are well below your target of 500 lines.