I really don’t know what the problem even is. Start by converting from diesel to Natural Gas. You achieve the elimination of almost all nasties and a CO2 reduction. Once the market and infrastructure are there, offer incentives to biogas and syngas producers to convert their stuff into bio-LNG. Voila, CO2 neutral LNG that can be used in the same infrastructure and vehicles as the fossil one. You need a market for bio-folks to find it worthwhile to invest.
A new paper from Carnegie Mellon University didn’t get much attention, but it tackles a huge topic: the challenge of cutting carbon emissions from the energy-hungry trucking sector. One takeaway is that trains can play a big role, but that would require a reversal of freight industry trends worldwide that favor highways.