Believe it or not, I have actually worked on a 604 Turbodiesel. It is one of only three or four in the state, according to the owner (and we have more Pugs here than in most places because we have a big Pug shop in town and a fair sized support community). I would be surprised if there were more than 50 of them left on the road here in the US.
The one that comes to our shop is actually a pretty neat car... it is a 4-cylinder turbodiesel with automatic trans, and over 390,000 original miles! It actually drives quite nicely. The engine is noisy outside the car but it's quiet inside and has plenty of power even with the automatic. It's a good runner. It was the first car I had driven in a long time that I liked almost enough to consider it as an alternative to a Volvo 700 series TD (though it didn't have that sweet straight six sound
). It rode and handled great. I see it around town all the time. Probably won't be too long before it comes in for its last oil change before it hits 400k...
If I were you, I would try to find a Peugeot TD drivetrain, or a whole TD car to swap parts from, rather than trying to shoehorn a 5cyl TDI in there. The Peugeot motor is very compact, since it's a pushrod design. The VW engines are quite tall, being an OHC motor with the cam set directly above the valves and bucket tappets in use, and the 2.5 TDI is probably even taller than the D24T since the D24T is 400cc/cylinder while the 2.5 is 500cc, which in the case of the 1.9L engine versus the 1.6, is achieved partially through a taller block (IIRC -- not sure of my memory on that but believe I'm remembering correctly). The ZF 4HP22L used behind the D24T was only ever available with a bellhousing set up for the 700 series installation position, which is the more straight up-and-down style. Volvo 240s with the D24 non-turbo engine used more of a slant in the motor's position, but they never used the ZF trans. The only automatic they ever got was the BW55, which is an old style 3-speed clunker with no lockup converter. I have driven them in NA 240 diesels and they are OK around town but would be no fun on the highway. The BW55 is similar in design to the later AW70/71/72 transmissions used in Volvo redblock gassers in the '80s and '90s, so maybe if you really cared enough you could somehow build a nice AW70L that would bolt up to a D24 or 2.5 TDI, but it would be a lot of work...
The other issue you will run into with trying to run a D24T automatic behind a TDI engine is that the shift points and converter stall speed will all be wrong... IDI engines reach their powerband at a much higher RPM than DI engines do, and they top out a good 500-800 rpm higher as well. Your 2.5 TDI's performance would not be optimized with a D24T's trans behind it.
I can measure a spare motor at work tomorrow for height.
A better idea for your situation might be to get a 1.9 TDI VW motor and install it with a big slant, to keep height under control (like it is in a modern Audi or Passat), then figure out a way to adapt it to a Peugeot transmission that will install easily in terms of mounting, driveline connection, etc. But the truth is, they work pretty nicely with the original style Peugeot drivetrain in there too, I can vouch for that... so going that route might be the easiest and turn out a lot nicer than you think.