Gosh dkenny. Obviously, your biodiesel knowledge is far superior to mine. You're absolutely right, I haven't made a single ounce of biodiesel...but I'm thinking about it. I've made a few kg esters based on undecylenic acid for work, but that experience doesn't count because it was at work and not meant to to fuel for my Jeep.
I'm really disappointed that my undergraduate education in chemistry nor my graduate education in chemistry didn't prepare me for the mystical nature of synthesizing biodiesel. I need to contact Missouri-Rolla and the Univ. of Michigan and tell them to add this to their curriculum so that their future alumni won't be as ignorant as I am. Ironically, in a court of law, I could be an expert witness on some topics because I have a PhD in chemistry, but in this case, I have to cite a bunch of textbooks and cite a gazillion literature references. Transesterification is an equilibrium process. It's very difficult to get 100% conversion. Until you explained it to me, I didn't realize that the chemical principles for esters didn't apply to biodiesel. Thanks for the chemistry lesson.
Here are a few things to consider:
1. Yes, KOH, NaOH, MeOH (EtOH, PrOH, i-PrOH, and BuOH) are either soluble or miscible with water. However, trace amounts of all of these will still be soluble in the fatty acid esters. When one wants to remove these on the laboratory scale, they typically wash the organic phase with brine. After a few times of that, they "dry" the organic phase with a hygroscopic salt such as Na2SO4 and MgSO4.
2. I'm not 100% sure what you getting at in #2 above other that having some basic catalyst and free fatty acid left behind can fall within ASTM specs. Does everyone who makes their own biodiesel rigourously test it to make sure it fall within the spec? The corporate guys probably make sure this is the case. Most individuals probably go on faith that if they follow the procedure, they make something within spec...and that's probably true most of the time.
"oh just for you info the biodiesel does contain some KOH/Naoh it will not contain FFA" is not necessarily true. If no water is present, the free fatty acid salt (note the nomenclature) will be the only thing there. However, when water is around, there is an equilibrium reaction at work: (free fatty salt with alkali) + (water) <equilibrium arrow> (free fatty acid) + (alkali hydroxide). You can argue, but if that base is present, water will be present too. It's nearly impossible to have one without the other. Your statement that "the mixture is basic in nature" is correct...due to the above equilibrium. The free fatty acid salt is a proton acceptor. In this case, water is the proton donor and is therefore acting as an acid.
Whether or not a substance will corrode steel is no indication of whether it qualifies as an acid or base. There are like 7 different acid-base theories. None of them include "things that do not corrode steel are bases." The two prevailing theories are Bronsted (molecules are designated as proton donors or acceptors) and that of Gilbert N. Lewis (molecules/atoms are electron acceptors or donors) Amines can promote corrosion of steel and they are basic. This is somewhat subjective too since different alloys of steel will have differing resistances to corrosion.
To really make a declaration of whether a metal will corrode, one could refer to a Pourbaix diagram:
http://en.wikipedia.org/wiki/Pourbaix_diagram Pourbaix was a maniac and constructed these phase diagrams for an amazing number of materials...must have sucked to have been one of his graduate students. You already established that a biodiesel mixture will be basic if anything, so if the if the electrochemical potential is in right range, there is a possibility that the metal in question could corrode.
3. Dude...I was asking a question. I know DIY's recover the biodiesel based on density and immiscibility. Most people aren't going to have equipment of sufficient scale to do efficient distillations. However, a large commercial facility could. I was asking based on curiosity. I wasn't making a declaration of how it was done.
4. "adding an acid to biodiesel will cause a reverse reaction..IE you'll make FFA's(acidic in nature) from biodiesel..BAD!"
This isn't necessarily true. It kinda depends on the acid and how one carries this out. If I neutralized with acetic acid (vinegar minus the water component), it wouldn't be a problem. The pKa of acetic acid won't be too different from that of the free fatty acid and it wouldn't catalyst the reaction. Now, if one used sulfuric acid, it could be a problem. However, the proposition was to "neutralize" the mixture, not make it acidic. And even one was to make the mixture acidic with a strong acid, it would be okay as long as there is minimal water present. If one overshot, you could just neutralize with baking soda (sodium bicarbonate)...just be ready for the CO2 evolution.
FYI...a very common method of performing an esterification or transesterification is by using a strong acid as a catalyst instead of a base. This usually works better because it's a little more tolerant of water.
I'm not sure what JFT is...I'm guessing "Journal of Fuel Chemistry and Technology" ???? Usually if something is a peer reviewed journal, the information is generally accurate.
5. "all oils will polymerize...gee do you like polyurethane for a wood finish...but you wouldn't think about pouring into you fuel tank..what about something closer..boiled linseed oil...nice finish but a lousy long term fuel..short it'd be fine..but what's short..that's right it depends...diesel and gasoline have shelf life's...well so does biodiesel..and somethings shorten this life"
It depends...you just can't declare that all oils will polymerize. I work with silicones. Those don't polymerize unless they're treated under extremely harsh conditions. I think polyurethanes are great wood coatings. They also make a great resin for the topcoat on a lot of cars. Love 'em love 'em love 'em, but I wouldn't put it in my tank. Oils that are completed hydrogenated won't polymerize. And as you pointed out, linseed oil does polymerize, because it's unsaturated.
Gasoline and diesel have respectable shelf lives because of their processing. Diesel is distillation cut of crude. This is a good first step in terms of purification. Both gasoline and diesel are hydrotreated to remove sulfur. A bonus to this process is that it removes the non-aromatic unsaturation and therefore "removes" the components that can undergo polymerization.
6. Probably the smartest thing you said in your entire critical analysis of me was: "It's all about oxidation!" There's no denying that. However, oxidation can be viewed in a few different ways. Just read this:
http://en.wikipedia.org/wiki/Oxidation
Cu and Zn aren't really good complexers of double bonds. Their oxidation/reduction process is likely separate from what happens to the biodiesel. For biodiesel, it probably comes down to the unsaturation and presence of oxygen. I have an interest in biodiesel too, and I've pondered how I would reduce the oxidation of my product if I was to make it. There are two simple things you could do:
i.) Get a tank of N2 with a regulator and sparge you tank or drum of biodiesel product. This will displace the dissolved oxygen. Getting rid of this would severely retard the rate of oxidation and lead to increased shelf life. If one wanted to be extra fancy, they could leave the N2 hooked up so that the storage vessel always has a blanket of N2 over it...I would only do this if I had a relief valve that kept it the pressure under 2 psi or something like that. We don't want to be popping drums due to overpressure.
ii.) You could literally add an anti-oxidant. Vitamin E is very commonly used. My company, for instance, uses it to increase the shelf life of many of its personal care products. With an appropriate amount, things survive some pretty harsh accelerated aging relative to the control. It acts as a radical scavenger and helps suppress the polymerization reactions. So, when you buy your drum of MeOH, have them send you a gallon of Vitamin E too. I don't know how much would be required. I would guess on the order of 500 ppm would be a good starting place.
I usually let these things go, but it's not that you came on strong...you came on strongly ignorant. You might find boning up on your organic chemistry would be of benefit. Throughout my education, I learned of all kinds of things I didn't know. I would generally reach out to someone like you for practical advice on how to make biodiesel. I couldn't bring myself to do that now no matter how many years of experience you have.
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4/11)..Bus gone to Scarp 8/23/11 
dkenny
At least conditions would be right in a few weeks for dkenny and I to have our snowball fight.