I've done some quick number crunching and here are some of my conclusions:
Overall, the conversion box is designed to give players bonus in Omega Marks, not Borg Neural Processors. In fact, the number of Borg Neural Processors is capped at a maximum of 15.
As many have noticed, there are about 15 conversion tiers.
Tiers 1-4 seem aimed at players who run normal (non-elite) STFs. Specifically, only in tiers 1-4 are Rare Salvage factored into the conversion calculations. From Tier 5 and beyond, all my regressions indicate Rare Salvage are either given somewhere between 0 to 10% weightage in tier calculation.
The little bit of good news is that at lower tiers, the EDC/salvage to Omega Marks conversion ratio is very good. At tier 1, you are getting 12.5 normal STFs worth of Omega Marks in exchange for 1-10 EDCs. The bad news is that bonus quickly becomes a conversion penalty at around Tier 5-6 where you loose out on a significant number of Borg Neural Processors and dilithium.
There is some indication that the STF accolades and/or number of STF runs play a factor into the quality of the box you get, especially at lower tiers. So even if you only have 1 EDC, it is very possible to get a tier 2 or perhaps even tier 3 box if you have > 40 of STF runs and a few MACO/Omega Force/Honor Guard accolades.
My conclusion is this, try to aim for either the tier 3 or tier 4 box for the optimum conversion rate. If you have a few STF accolades and around 15 EDCs, you should be able to get the tier 3 box which contains 1000 Omega Marks and 5 Borg Neural Processors. If you have around 20-40 EDCs, 10 Rare Borg Salvage and 10 Prototype Salvage, you should be able to get 1500 Omega Marks, 7 Borg Neural Processors and 1000 dilithium.