Q. Can you think of any additional literature available on how to calculate/assess risk, not written by a government agency?
A. There are many books and articles that deal with that, especially from the statistics and probability point of view.  Here are two:
http://www.amazon.com/Fundamentals-Risk-Analysis-Management/dp/1566701309
http://www.amazon.com/Theoretical-Mathematical-Foundations-Health-Analysis/dp/146137815X/ref=sr_1_sc_1?s=books&ie=UTF8&qid=1423101241&sr=1-1-spell&keywords=theoretical+andmethematical+foundations+of+human+health+risk+analysis
But, as a practical matter, most clean-ups must meet government standards, regardless of theory or science.  See also my chapter in toxicology: http://www.raperkins.net/ENVE_652/Module12/12A_RegulatoryTox/12A_RegulatoryTox.htm
The field of systems engineering deals with the risk of failures.   For our interest, the effect of chemicals from the environment, we deal with many uncertainties in both the toxicity and in the fate and transport. 

Q. What do RA/SI and PI mean?  In the 2011 closure, the second question asks about phases I don’t recall seeing in the module: the RA/SI and the PI.  The quiz also added PI/SA but I think that is red herring.
A. Those are terms of art from the EPA Superfund process.  But, the concepts are universal.  PA/SI means Preliminary Assessment/Site Investigation, which could be the first few site visits and enough thought to get some budget to do more.  RI/FS, “riff is” means the Remedial Investigation, where the site is sampled, drilled, etc., and Feasibility Study, where the various alternative are examined; RI/FS requires budget.. 
See bottom of http://www.raperkins.net/ENVE_651/Module02/2A_RA_laws_and_regs/Module_02_2A.html

Q. I read through chapter 4 of McKay’s Mulitmedia Environmental Models and was curious if the calculations take into consideration things like permafrost?
A. No.  Nor does it do groundwater.  We have another program for that.  Permafrost diverts groundwater flow, but does not really affect contaminants otherwise – that I know of. 

Q. The groundwater is also very cold and I have heard that contaminates have a much longer lifespan due to the colder water temperature upwards of 50 years longer than in groundwater temps found in the lower 48. Is there any validity to that assumption?
A. That varies with the contaminant.  Some bacteria can operate at very cold temperatures.  If there is a steady source of contaminant that is amenable to degradation, the bacterial community will adopt to degrade it.  The degradation involves burning the contaminant for energy and making biomass – new bacteria. 

Q. Does “Long John” now “own” the contamination (and all of the associated costs of cleanup) even though the PCBs likely migrated into his harbor from upstream sources? Obviously the tributyltin can be attributed to the harbor.  However, PCB-contaminated soils are expensive to dispose of.  On a related note, if there were a USACE permitted dredge material disposal site out in the bay, he could have dumped away, right? So just by putting the dredge material on land he created a hazardous waste?
A. lI constructed the problem to emphasize the transport of the chemicals. But now, Long John does indeed own the pile and its contaminants.   As a practical matter, you can’t dredge without a permit.   The permit is joint with EPA and the Corps of Engineers.  Long John would not be allowed to dredge without a proper site for spoil disposal.  Likewise, if there was an approved site, it would only be for clean materials and you would have to have a sampling program to prove it was clean – below the regulatory standards. 

Q. My criticism is evident in the answer I provided for my chemical search above. I use Google almost exclusively, and I’m pretty sure it is the most popular search engine. Wikipedia almost always comes up first for chemical searches, and the top five non-wikipedia pages are usually government sites (EPA, NIH, CDC, IARC). I’m not sure I’m grasping the point of this exercise. Maybe I should use a bunch of different search engines and see what results I get, but the Google results usually seem pretty relevant.
A. Yes, Wiki has it all.  If it’s important, I look at the references at the bottom of the Wiki site. 

Q. I don’t know if you will be able to answer this questions but it is regard to a hazardous waste and a hazardous substance. When a refined petroleum product or even a crude oil is released and cannot be recycled I would assume that it then goes from being a hazardous substance to a hazardous waste. However, it does not appear to be considered a hazardous waste under RCRA. Do you know why that is?
A. Petroleum products were exempt under the RCRA law.  However, if a component, say benzene, is over the toxicity limit on the TCLP, the waste is hazardous under RCRA.