You will likely find that the logistics of keeping both Vipers and Reapers is not really worth it. The performance characteristics are just way to similar. The designated AMM can hit a target that is moving 10k km/s with 22.5% likelihood- while the MPM can hit it with 21.6% likelihood - just 0.9% less likely. If you really find a reason for a 6m km missile, you might as well make it the standard range of your AMMs. The 0.9% less hitchance is a small price to pay for greatly reduced logistics, research effort etc.
Also remember that firecontrolls and missile launchers can be freely assigned to each other, even during combat. Since you want to go for integrated ships, you will likely have further reaching firecontrolls anyway. These can be linked to the size-1 missile launchers. In other words, if you wish to have a "secondary" anti-ship missile that can be launcher from the size-1 launchers, you can increase the range beyond the maximum range of the smaller FCs without much of a problem.
You active search sensor is too small (or your FCs are too big). There is no point in having FCs that go further than the search sensor can see, as you can't engage targets that are not "illuminated" anyway.
