I'm in the final stages of doing this (although I started with a Toploader) on my '66.
What engine do you have? If you have a V8 with a 6 bolt bellhousing you'll be able to bolt up a late model T5 bellhousing. If you have a 6 cylinder or a V8 with 5 bolt bellhousing then you're almost certainly going to have to find a used 65 stock manual shift bellhousing and use an adapter kit to attach the transmission to the bellhousing. If you can use the T5 bellhousing, it's a bit less expensive and easier and you should buy one with the transmission.
You need to decide how to actuate your clutch. You can use the stock-type bellcrank, a hydraulic setup or a cable. I went with a cable but wish I'd kept the stock bellcrank (the cable kit I bought requires you to pound the pogies out of the underside of the cowl to make room for the quadrant on top of the clutch pedal and you also have to cut a new hole in the firewall). To use the stock bellcrank with the T5 bellhousing you'll need the bellcrank, attaching hardware for the engine and frame, a fulcrum kit and a stock-type clutch fork. If you go with the cable you'll need to use the T5 stock type clutch fork (goes with your bellhousing). Oh and for the T5 bellhousing you'll also need the clutch lever cover and a clip to hold the cable at the bellhousing (You can get these at most hardware stores - it's just a large C-clip). I bought the cover and the clutch lever on eBay.
You'll need the manual shift pedals and any associated linkages that you expect to use.
You'll need a transmission. The World Class T5's are generally considered the best. You can find them used on Craig's list. Before you buy, find out what the tag number is - this will tell you what the transmission gear ratios and torque capability are (http://www.fordmuscle.com/archives/2000/09/t5swap/index2.shtml
). Others have suggested that when you look at a transmission make sure it shifts into all gears, that the input and output shafts turn smoothly with no hitches or glitches, and that there are no bad smells at the input or output shafts. When I looked at the one I bought I also had the seller pull the fill plug and sniffed at the insides to see whether there was any hint of burn.
You'll need a block plate, flywheel, clutch, throwout bearing and pilot bearing. The type of throwout bearing will depend on how you actuate your clutch - the stock T5 bearings are a lot different from the type used in the stock 65 clutches.
You will also either need to modify your transmission crossmember or buy one of the aftermarket units. Modern Driveline sells one that's supposed to be pretty good - I have one on the way. I'd bought one from someone else but found out that their design did not allow it to clear the exhaust routing so I've had to try another brand. Hopefully the new one will work better.
You may have to have your driveshaft shortened.
You will have to bypass your neutral start switch.
You'll need a shifter (unless the T5 you purchase comes with one) and a shift lever (the stock T5 shifter levers are short and will be a pain to use if you don't change to a longer one).
Hope this helps a little and that your conversion goes well.