Regarding EPA emissions tiers, I was under the impression that railroads under a certain size may be exempt (or partially exempt) from those standards, but I could be wrong... clarification would be welcome.
If the standards do apply to PAR, I would assume that the locomotives only need to meet Tier 0, which applies to locomotives built before 2001 but after 1972. (all the pre-Dash-2 stuff would be exempt, I guess.) My understanding is that Tier 0 is relatively easy to attain in a turbocharged 645 locomotive, especially if you were going to rebuild it anyway, because one of the things you need to do to meet Tier 0 is rebuild or replace the power assemblies and injectors — something most railroads would do by default during a major rebuild.
HELM, which PAR seems to have a good relationship with, sells kits to meet the various EPA tiers:
http://hlmx.com/bolt-on_emission-kit.asp" onclick="window.open(this.href);return false;
Similar kits are also available from NRE, GE, and others.