The 727 does not have as low of a first gear, so if your Eagle has 2.35 gears or larger tires (or both), you will be rather sluggish off the line.
There is absolutely nothing wrong with the strength or durability of a properly built 904/998/999 automatic transmission. First of all, the auto transmissions are stronger than any manual used in Eagles in terms of torque and hp ratings. I agree that the lockup torque converters are known to snap with incorrect fluid use or heavy application, and that they may not have been the greatest from the factory because of this. However, a rebuilt 727 won't necessarily last you any longer or shorter than a rebuilt 998, unless of course you swap in a V8 or stroker with 300+ hp.
The non-lockups were often favored because of poor designs of the early lockup convertors. A properly functioning lockup convertor on the other hand will create less heat and run more efficiently. Walmart now sells Valvoline full synthetic Dexron transmission fluid for ~$18 a gallon which would be highly recommended.