My Pinto is starting to piece together at this point, and the only thing really left missing is the T5 and bell-housing.

I know they made the T5's for the 2.3 Mustangs, and they had a lower first gear to compensate for the lower power from the motor. If I recall correctly, they weren't as heavy-duty either compared to their 5.0 brothers.

So, my question is, is there any other differences? Would it be possible to run a 5.0 T5, with the correct bell-housing, and compensate with different rear-end gears to comp for the taller first gear in the tranny?

One reason I thought about this, was because the motor I am throwing into the car is going to be a little more powerful than a stock 2.3. I would think the 2.3L T5 should be able to handle the added power, but obviously the 5.0L one would be a little stronger behind it. Maybe I am just over-thinking and worrying too much. I tend to over-build things just-because and for the added peace of mind.

Or is this just a bad idea, and should I seek out the 2.3L T5. I would assume the 5.0L versions are easier to come by, and be a little beefier.

Transmissions are rated by torque capability, not horsepower.
 
1985-89 Ford T-5s, V-8 & 4-cylinder, are rated at 265 ft-lbs.  Many V-8 Mustangs were severly beefed up, with little or no problems with this transmission.
 
1990-up V-8 T-5s were rated at 300 ft-lbs.
 
IMO, a good condition 85-up 4-cylinder T-5 will handle just about anything you can throw at it in a street driven car.  A 400 hp 2.3T will have a much lower torque rating than a 400 hp 5.0 and the transmission should readily handle it.
 
Of course, as with just about any internet advice, Your Mileage May Vary.   
 
Mike