Rear Axle:
Used stock car parts. You'll find a number of stock car rear ends out there from 55-60" hub-to-hub; 57" is perfect for early Fords (pre-67). Don't waste time trying to find a Versaille rear end, you won't. They didn't build many Versailles to begin with and they're basically all crushed now.
I wouldn't bother shortening an 8.8, none of the 8.8s Ford ever built are narrow enough. An Explorer 8.8 is the narrowest and it is still 6" too wide. By the time you futz with it, money won't be saved. While there is technically space to have a wider axle up to 60", you'd do better to err on the side of narrower, not wider. The rear wheel wells will limit you tire wise with a 57" axle to 225s. If you go 55" you can get 255s under the car by rolling the fenders. A 60" axle is going to make you run an odd offset wheel and you'll probably only be able to get 205s under the car.
If you're a junkyard cruiser, look for a good 9" center section and order a housing to your width from Speedway and cut-to-fit (short) axles. For ~$6-700 or so you can have your 9" that fits perfect under the car.
Edit A couple of Hours Later to Add:
Check your rear axle, I'd bet money if the car codes as a 289 car it has an 8" rear axle. They only put 9" in HiPo (K-Code) cars (in '65), but C-Code cars typically got 8" axles. You could easily rebuild the 8" with 31-spline axles and a limited slip and unless you're in the habit of doing clutch drops with 500 ft/lbs of torque on tap, you're not likely to break it.
You can check it easy, if it has a drop out center section, it is an 8" or 9", if the center section is integral and there is a cover on the rear it's the smaller 7.25" rear axle. To determine if it is an 8" vs. 9" (they look similar from the eye), use a socket. If the center section nut at 6'oclock can have a socket put on it, it's an 8", if you can only get a wrench on it, it's a 9".
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Brakes:
Square Body Falcons did have discs available. All of the '64 and '65 Sprints did and they were an option from the factory.
However, this is a later conversion. All Ford front disc calipers used in the Falcon/Mustang/Comet/Cougar/Fairlane from '64-67 were 4-piston Kelsey-Hayes. In '68 they went to a single piston design, these are the single piston design. That's a '68-later setup and it could be from almost anything, later Falcon, Mustang, Cougar, Comet, Maverick, Grenada, Versaille, etc.
Dual bowl master cylinder wasn't standard until '66/'67, so that's also a conversion. Though a common one when swapping to front disc brakes. Edit: Every single Ford master cylinder from 1960-1995 for cars and light trucks have the same master cylinder footprint. So it's no uncommon to find a later MC on an older car. If you need an MC they are easy to get.
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Valve Covers:
Those are late '60s square/pent-roof style. Commonly found on Mustang/Falcons/Torinos/F-series trucks. When sand blasted and cleaned up, they look great wearing a coat of Ford Blue. But originals would have been round top and probably Autolite Gold.
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Bolt pattern on block:
5-bolt blocks were used in '63/'64 across all 221s, all 260s, and on early 289s. I haven't seen a '65 with a 5-bolt block, they went to the 6-bolt late in '64 early in '65. The 6-bolt is the same pattern as all other SBFs from subsequen generations. If it turns out it is a 5-bolt block, Modern Driveline makes a bellhousing conversion to mate it up to a T5.
If you want to do a T5 swap, save your pennies and order the kit from Modern Driveline. The shifter of a Mustang T5 will come out too far to the rear, directly next to or even behind you. Then you're in the bag for doing a tailshaft swap to a forward mounted shifter S10 tailshaft. I've been there and gotten the t-shirt, these parts are getting HARD to find (like a Versaille rear axle). Guys who are talking about their conversions were buying parts 20-25 years ago now, today the expensive of finding the parts and DIY'ing a conversion just doesn't make financial sense, unless you happen to have or know of where to find the parts.
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I know it isn't the most 'grassroots' way of doing things to throw money at the problem, but when it comes to classic Fords all the parts, upgrades, etc are available and relatively inexpensive compared to other marques.
I miss working on these old Fords, I've had two Mercs (Comet and Cougar) and a Mustang. One of these days, I'll get another, I almost had the Mrs fully onboard with a Falcon Ranchero. But I really need to focus on one project at a time and four cars for two people is one too many (I know that's GRM antithetical too).
