First I want to congratulate you for taking on a big task like that. It looks like you have a quite sound car to start with and I'm sure you'll enjoy continuing your dad's project.
The thing to remember is that it's your can and you can do whatever you want with it. That being said, I would second the opinions of others that keeping it as stock as possible is a reasonable way to start out. Heck, you may like it the way it is and keep it that way. I've had my '72 since 1974 and just got it back on the road after a multi-year hiatus and it still looks, and drives much the same as it did when it was new.
I have a couple suggestions. If you don't have one already, get a factory shop manual (FSM). It will save you hours of searching and avoid mistakes.
For your rust mitigation - what I did on mine was wire brush/sand to remove loose rust and paint, then brushed on some Locktite Extend Rust Treatment. It a rust converter, you can Google it, that leaves a primed, paintable surface. It has held up for the last 12-14 years on the under-body components, gas tank, suspension parts, etc. This was much more convenient and less expensive than powder coating. There are other brands of similar concoctions, maybe others are better, but I was happy with this one. That way you could have the rust mitigation done before it goes to the body shop as a rolling chassis.
Another thing to think about - if the car has over 75K or so miles, the throttle shafts are likely worn. They are chrome plated brass and soon wear down so as to allow air to leak around them, making tuning impossible. Also, the worn shafts make the gas pedal feel "sticky" when first pressing down. The solution I wound up with was remanufactured carbs from Z-Therapy. I fooled around with the old carbs for years and finally came up with the $$ for them. It took a couple months for them to fill my order, which was a bummer, but it was worth the wait. The throttle shafts now have sealed roller bearings and are smooth as silk. I couldn't be happier.
My only guess for the odd ball fan by the fuel lines is that your dad had a problem with vapor locking judging from the insulation on the fuel lines by the carbs. I tried that on mine too. Anyway, I've found that living where I do at 7,000 feet altitude, the 240 and my '78 280 run better on non-ethanol gasoline, no hot-starting issues. Not sure if you can get it where you live, but if you can get it, give it a try.
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