Hello Graham – I don't post very much these days but always willing to help another engine maker when I can.
All the 5cc engines I have made so far have had all major ali parts from 6082 (He30) . This machines very easily, takes a good thread and, if required, anodises well. As already said and like Jason I only use a higher strength – 7075 or He 15 for the conrods.
I have a scaled 5 cc Nalon Viper 'on the cards' – the cases are made, as said, from 6082 which I'm confident will be more than strong enough.
The Model Engine Boys drawings were done by Model Engine News owner Ron Chernich from, I believe, an original engine – I would assume he called out the spec on the case parts to suit his views. Personally I would not have thought a higher strength than 6082 would be necessary for the case parts even if the engine is to be used in the team race environment as originally intended but of course if you have the material then why not.
I have just looked for 6061 on ebay – there is plenty of choice at reasonable cost but it appears to be mainly round section.
Hope that helps some – good luck with your Viper – is it destined for a vintage T/R BTW?
Regards – Ramon (aka Tug)