One of the main issues with the MEL series engines used in these Lincolns is that they used three different bell housings depending on the year.  The early 383, 410,  and 430 MEL engines from 1958 through 1960 used the same bell housing pattern as the FE series engines 332, 352, 390, 406, 410, 427, 428.

From 1961 through 1965 the Lincoln 430 used a modified FE pattern.  The starter location was moved to clear the new for 1961 Lincoln unitized chassis. That pattern looks like this on the back of the block :

430 MEL/FE Pattern

In 1966 the MEL engine was enlarged to 462 cubic inches and the transmission was changed to a C6.  The Lincoln Chassis was altered quite a bit, among the changes were the firewall area around the heater box to clear the new larger C6 transmission.

1966 – 1968 462 engines have a third bell housing pattern.  The pattern rounds off on the passenger side for clearance, however the 462 blocks themselves have both the 1961 – 1965 pattern and the 1966 – 1968 C6 pattern.  The back of a 462 block looks like this :

The short answer is no, a C6 transmission from a later model 462 will not work behind your 65 Lincoln 430; unless, of course, your 430 block happens to have both patterns like a 462.

Lastly, you can get a transmission adapter to put either a Chevy transmission or a later model Ford AOD.  You can see the pricing here : http://www.transmissionadapters.com/Pricing.htm

You know, I always forget the Cruise O Matic has a removable bell housing.  It’s possible it might work with a bell housing swap.

Let me research this a bit and see if I can find a definitive answer.

From everything I’ve found browsing around the Thunderbird and Lincoln transmission are different.  The Lincoln is a large case transmission and the Thunderbird uses a medium sized case according to the folks I talked to.  However, I’d put them side by side and give them a good looking over to make sure.

Good luck!