You have several options.
The junkyard bolt in option is the Lincoln Versailles rear end, but brake parts for this housing are becoming increasingly difficult to find, not too mention that it's still older technology.
The other option is the bolt in complete rear, from Currie Enterprises or other manufacturers. They will build you a rear to your specs, with either 11" Explorer rear disks, or a wilwood setup. Currie is expensive, but you get what you pay for. They assemble everything for you, and you just slap it in when you get it, all brand spanking new.
There is a cheaper route to go, however. I purchased a brand new Ford 9" rear end, with 11" explorer brakes on ebay from "Quick Performance Racecars and Components" (see link below). The housing has new tubes, the correct length for my 65, plus spring plates already welded in place. Everything ships seperate though, and you have to assemble the rear yourself. It came with Moser axles, the explorer brakes, and a center section with any gear ratio i want. Also included are axle bearings, and all the other small parts. It was a hell of a deal, and hit me for about $1950 including shipping.
eBay Store - Quick Performance Racing: Spools, Housings, Ring Pinions Gears
sometimes he has complete rears for 65-66 on ebay, if not, i'd give him a call. i'm very pleased with everything i got.
Don't forget that with rear disks your going to need to do some other braking system upgrades as well.
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1965 Mustang Coupe Project: 1965 Mustang Inline 6 (For Now) Coupe, New Floors, New Quarters | Ford 9 Inch Rear, 11" Rear Disc Brakes, 3.50:1 Gears | Control Freak Front U/L Control Arms, Global West Adj. Strut Rods | KYB Gas-A-Justs, Grab-A-Trak 620 Coils & Mid-Eye 5-Leafs | Global West Tubular Subframe Connectors | Addco 1-1/8 Front Swaybar Kit