Hi Sausage - yes, I see your problem; Alfa transaxles are few and far between, and yes, you are correct, it is not possible to turn over the crownwheel and pinion to make a 5-speed rear-mounted gearbox. The only solution is to run the transaxle upside down to get the gears round the right way.
Conversely, VW transaxle is easy to modify this way - off come the side covers, out comes the CWP and Bob is your mother's brother
The VW transaxle was used as the basis for the first Hewland F3 'box, and is still available today (although Hewland do their own castings these days). For some reason the Hewland casing is used upside down, but they might do that to lower the engine CofG...
If your rear-engine trike is going to have two seats, if you can mount the rear seat high up over the transaxle (like the classic Wilmac and Ed Roth trikes), you might be able to fit two small (say Mini-sized) radiators behind the pilot - I've always thought some jet fighter style nacelles at shoulder level would look quite good, but I guess that isn't the "naked" look you are after
You feed the heated output from the engine into the bottom of Radiator 1, then feed the top outlet across to the bottom of radiator 2, then back to the engine. Electric fans and a thermo switch should do the rest...
I believe you are right, the 1303 'box has closer-spaced ratios than any other, but is still a 4-speed, so there tends to be large gaps between one ratio and the next (not as bad as the old 1500's though, they had a massive gulf between 2nd and 3rd...)
Do you have the VW rear suspension? The usual trick was to cut the VW floorpan just ahead of the torsion bar tubes and use the entire rear suspension and gearbox mounts - then cantilever the downtube and front forks off that. I'm no fan of Beetle chassis dynamics, but if the suspension is lightly loaded and the overall travel is small, it can be made to work reasonably well. On my friend's Nova (kit car) we reset the torsion bars so that most of the load is taken on coil-overs which replace the standard dampers. The coil overs allow fine tuning of the ride height and overall suspension spring rates.
Hehe - like Daz, I wanted to build a trike too. My interest was in the DG Phoenix (a European copy of the Wilmac), made in 1986. I got the brochure/instruction leaflet but never took it any further