First off make sure you are getting a good 6.0. From what I have read the 03 & 04 years can be a nightmare. Headgaskets, injectors, EGR coller etc. By 06 Ford seemed to have made the 6.0 a much better engine.
I would suggest you take some time & check out this site. POWERSTROKEHELP.COM - The Information Source for Ford Power Stroke Diesel Owners
I am pretty sure that converting the 6.0 is 99% the same as converting a 99-03 7.3. There are a few differences but not much.
Definetely keep the fuels completely seperate. Run an entire new fuel system for your veg. Use check valves in the heads on the diesel lines & a check valve in your veg system. You plumb in a solenoid valve right before the veg check valve & when you switch back to diesel you open that valve up which allows you to flush the veg out of the fuel rails with diesel & then run another minute to burn up any veg in the injectors. This makes for a very fast & efficient purge.
IMO you must at least have a fuel pressure gauge & a veg temp gauge. I would suggest a FPHE as you final heating device & plumb it as close to the engine as you can get it. Mine is on the firewall by the brake master cylinder. Yes get the Fass HPFP. It's a bit pricey but worth every penny. Either buy or make a heated pickup for your tank.
Have you looked at the Vegistroke kit? It is up to you but a DIY can be a major undertaking & at the end of the day you mau spend almost as much as the V3 costs. I did a DIY on mine which is working well but was ALOT of work to source parts, figure out where evrything was going to go, make a million trips to the hardware & automotive store etc.. etc.. etc.. I if could do it again I would spend the extra $$$ for the V3 & be done with it. Frybrid makes a very good system as well.
Hoepfully Clay will chime in as well. Do lots of reading on FRYBRID SVO/WVO FORUM an open and public discussion of Vegetable Oil as a fuel
They are both very good sites IMO.
2001 f-350 ext.cab. 7.3 auto non dually. 262k miles. New HD tranny at 67,000 miles. Boost, EGT, Tranny temp gauges. 04/10 DIY check valve VO conversion. 20 plate FPHE,Fass HPFP set at 70 PSI,TIH, 10 micron spin on filter with coolant wrap, 150 micron prefilter, hrydraforce purge valve, 40 gallon greasecar tank with hotfox, SS braided hose to heads, Oil temp, pressure & fuel level gauges. 110K miles on grease.
Monitoring with Torque.