Before you decide to go the V8 route, you need to do a search on I6 to V8 conversions. A 351w can be installed in any 65'/66' stang (did it-see sig), but, as mentioned by rbohm, the I6 rear end will not be strong enough and the I6 steering/brakes/
suspension are too weak. All these items should be updated to the same parts as found in the V8 counterpart.
The original manual transmission used with the 351 would be the 4 speed toploader. They can also be found behind 289's, 302's and 351 clevelands. The bellhousing and clutch assembly can come from the same engines.The toploader for a big block is similiar, but uses a shorter input shaft which makes it unusable as is. A T5 conversion may be of interest to you, but you should do a search for that too.
The 351 will use many of the original V8 installation parts. Motor mounts, bellhousings, clutches, shifters, z-bar, and carb linkages, can be from a 65/66 289.
As far as problems with actually installing the 351, there are just a few. Alternator mounting brackets are 351w specific, although pulleys are interchangeable. The 351w needs more air flow than the stock 289 radiator can flow. Most who do the conversion cut up some of the radiator support in order to install a larger radiator. Finally, the exhaust can be a problem. Special swap headers are a necessity because the 351w is both a little wider and taller than the 289. The stock cast iron 289 manifolds will work, but are sinfully restrictive on such a big engine.
As first mentioned, you should first do a search and then decide if you have the skills and still want to spend the time and money to do the conversion.