The standard engines for a 72 Cougar was the 351C-2V, optional was the 351C-4V. There's nothing really wrong with a nice healthy 351C!
The standard automatic trans for a 72 was the FMX, with the C-6 being optional. FMXs and C-6s were found behind 351C-2Vs and all automatic 351C-4Vs were C-6s.
Now, with that said, the 72 Cougar is the same as the 71. They put 429s in a few 71s! A 429 uses the same block as a 460 (they're in the same engine family). There are lots of stroker kits for 460s that you can use to make it as big as a 566! The most common is a 514 cubic inch kit. The problem is that these engine kits are really meant for race duty and really aren't made for the street. Reliability and durability just aren't there for a street driven car. Anyway, a 429 or 460 is nothing to sneeze at!
Transmissions. If you put a 429/460 in your Cat, you'll need the trans that fits one. They only used C-6s behind them, unless you want a toploader four-speed. The C-6 has a one-piece trans case (bellhousing and trans case). The 429/460 shares a bellhousing bolt pattern with the 351M/400, so you can generally find a C6 to fit one relatively easily, just don't get one from a Lincoln since that uses the weird tailshaft/rear trans mount!
There are exceptions to the C-6 'rule'. My one buddy is running a FMX trans behind his 514-inch stroker motor in his 71 Mach 1. FMXs have a separate bolt-on bellhousing. He used the bellhousing from a 351M/FMX car I once had. He hasn't had any problems with this arrangement at all!