Hi Lewis; Nice to hear my bike is an inspiration...
I can answer most of these questions - so here goes...
1) I think Merc have stopped trading on the UK ebay for the time being - hence your lack of luck finding parts (I think EvilV bought them all!
). She's still registered as a seller so this might change - you could try contacting her directly - she may still have one lying around.
However - an alloy tensioner isn't necessarily mandatory. After having more than my share of chaindrops I took mine off and switched it out for a Brompton 2-speed derailleur (thanks somnatash!) that has deliberate side-to-side play on the jockey wheels that better works with the not-quite-100%-accurate chainline I was running. I say 'was' as I've recently upgraded to a shorter-axle bottom-bracket that fixes the chainline.
I think the main reasoning behind getting the alloy one is that the Merc plastic one is pretty cheap; the Brompton ones however are pretty well engineered and not something you should automatically disclude as a parts option on your bike.
Are you planning to ride fixed?
2) Yes I do understand that 355 wheels can be used - there's a white japanese one in a thread entitled 'best looking brompton' that I think has them. found it here
. I don't recall whether the rear triangle needed any mods to make it fit but the front should take them with skinnys with no mods at all. Discount any ideas about fitting any mudguards though
It has been reported that Moulton so-called 17" wheels (ISO 369) can be fitted with a little persuasion. I think that this must be with the ultra skinny panaracer tyre (and ultra hard to find)
3) it shouldn't mess up the handling. It'll feel a teeny bit more long legged with bigger wheels, though this will be a negligible effect; The fold should be fine too as we're only really talking about an increase of 6 mm to the wheel (that's only 3mm on either side of the axle).
Re better braking - I recently made some pretty unobtrusive drop-bolts so I could fit some rather elegant Campag Centaur skeleton calipers on the front - I must post some pix at some point; They work very well - if your bigger wheel choice is primarily about fitting shorter reach brakes, then don't rule out drop brackets/bolts.
Good luck with your build - I'm very interested to see / read more about it once you get it off the ground...
 here's another thread with a cool B with ISO 355 wheels:
Terrific 18-speed brompton MOD