CO2 sequesterization at the power plant level takes about 10% of hte net energy to get about 70% of the CO2. In this case the CO2 is pumped into deep (2000m) wells.
To get this to happen at a transport level, you need to convert CO2 into a liquid or solid. This isn't unreasonable: We store CO2 in fire extinguishers all the time. So the gas station would just pump out the CO2 when you pump in the gasoline. This would be roughly comparable to the tech used for propane fueling.
Someone who knows more chemistry than I do can speak to the irreducible energy cost of separating the CO2 from the exhaust.
The other part, the nitrates, are already done with diesel engines. You add urea to the exhaust which breaks down the NOx. Sulfates are mostly an issue with what is in the fuel. Low sulfur fuel is now mandated by law. I don't think it's currently an issue in North America or Europe.
This however may be the hard way.
A: Convert fossil fuel to electricity, with CO2 scrubbing.
B: Charge electric vehicles.
This eliminates the problem of carrying around a huge apparatus on each vehicle that is only used part of the time.
At present coal fired power generation is at best something like 50% efficient, with older plants being in the mid 30's. There is a possibility for solid carbon fuel cells. This is a non-thermodynamic process potentially 80% efficient. CO2 is produces as a pure gas make sequesterization much easier. To make this work, however you need very pure carbon. Not quite ready for prime time.