I have a 68 200 cu 6with a bunch of Clifford parts. I'm wondering if there is a new od trans that will bolt up to my 200 ci 6?  

I saw a 1966 Mustang 6 cyl car equipped with a T5 overdrive 5 speed at a show.  I have no idea what it took to get it in there.  

Ford used the same bolt pattern on pretty much all their transmissions after 1965. Its not a problem to get them to bolt up, but input shaft length, balance on flywheel and flex plate amd also torgue converters do vary a lot. If you use the bellhousing off the donor trans you have a better chance of succes. There are kits for the T-5 which is a good choice, I have not seen one for the AOD. But Keisler Eng. is a good place to look. I think for the AOD you would need a compatible convertor and shift down kit at least. Also take note that a lot of the newer trans's like the T-5 and AOD are a little longer so you will need to shorten your driveshaft.