Good post, and I can contribute to it with direct experience of having both LH 2.4 ('89), and 3.1 ('91) 245's, both with M47's. I also had both cars set-up with complete IPD suspension, custom exhaust and intake, and VX cams. I actually removed most of the mods from the 2.4 car to put on the 3.1 after the '89 was totaled.

The 3.1 is decidedly better in gas economy in it's stock form. It also runs much cleaner (it actually ran a smog test with 0.00 %CO at idle and 2800 rpm, 6 ppm HC, better than my '04 V70 2.5T, which is a ULEV car!). The 2.4 car is not as clean.
The LH 2.4 is known to be adaptive to performance modifications like increased a/f flow, can compensate ~20% from a stock set-up. My experience with 3.1 is that it's not only as adaptive, but tunes much faster than 2.4 with changes like gas octane. It can really perform if you use high octane and a hot cam.
The 3.1 has a different feed into the ICU than 2.4 and uses throttle sensor position to give a better advance than 2.4.
I'm currently running B234F 16V injectors, coil, ICU and 4 bar FPR on the 3.1 and has adapted beautifully to it. It is a MUCH better running car than the '89 with the same mods, and still gets 31 mpg on then highway, 25-6 mpg round town. The 2.4 would do 28-29 at best, and round town was 22-23 mpg.
The 3.1 has a better, smoother rev up to redline, and has no problem taking 3rd gear to redline at 90 mph. I had it on the Texas Motor Speedway a few weeks ago and kept it above 5k rpm the whole time, lots of power above 5k to push into the corners, something the '89 2.4 could not do.
I've wanted to do more internal modifications to the '91, but the motor is at 265k mi now, and never been opened. It runs so well, I just don't want to mess with a good thing.
--
'89 245 sportwagon, destroyed by hit & run driver, RIP. '04 V70 2.5 T Sportwagon, 12k mi and '91 245 5-speed, 209k mi, replaced the '89