Prices and Costs in the Railway Sector is a handy quick overview of very rough estimation for non-American rail costs. It's in 2000 Euros, which traded at parity with the dollar, so a simple inflation adjustment is all that's needed to bring costs up to today.
SNCF practice is to use a 60MVA substation every 40-60km and 10-15MVA autotransformers every 10-15km. These are the priciest elements of electrification, but not terribly so. Road overpass reconstructions to create clearance for electrification accommodating double stacked freight is almost certainly going to create major costs in excess of the actual electrification.
Catenary is sufficiently cheap (~$400,000 per track-kilometer) that any argument based upon the notion of delaying electrification because later improvements would require removal and reinstalling catenary ought to be ignored.
Purchasing ALP-45DPs without major modifications might be only 7.8 million per locomotive. Admittedly a high estimate compared to major freight locomotive purchases, but more affordable than their initial cost.
Amtrak's FY reports report a fuel consumption of 2.3 gallons per train-mile, but cost of diesel fuel is accelerating quickly. While Amtrak’s average for the year was $2.76 per gallon (for a total cost of $6.348 per train-mile), by September 2011 that had sharply risen and they were paying $4.38 per gallon ($10.07 per mile). Metrolink has currently secured fuel at a price of $3.25 per gallon and budgets at $3.40 per gallon in the current fiscal year ($7.48 and $7.82 per train-mile). Meanwhile Amtrak's 5 Year Financial Plan estimates a 6% annual increase in the cost of diesel with a price of 3.91 by FY2016 (page 45). I think this is probably on the optimistic side.
The British government sometime ago made available a study with a variety of actual fuel and electricity consumption figures for British trains. Of course they've redone their website since then and broken all the old links to it, but trawling around found it once more. 500 tons is close to the weight of a 6-7 car train set with American cars. Given LA Metro's price of 12 cents per kilowatt/hour, using electrical consumption figures from the Class 90 (22.62 kwh/mile), electrification with locomotives would drop fuel costs by two-thirds. EMU electrical consumption figures vary widely, down to as low as 5.7 kilowatt hours per mile, but also often being as high as a locomotive hauled consist. Off-handedly I want to suggest that third rail electrification may be more energy efficient than overhead.
Eyeballing the acceleration given in this presentation suggests a possible 20% improvement by use of electric locomotives over diesel. That said, I did not account for any difference in power capabilities.