... ford never did learn how to build something that wouldn't start rusting faster than it depreciated in value 
Seriously though, here is a small list to keep an eye on (from my experiences)
Rear doors - bottom of window and bottom of door
Rear Door mounts - Werent Strong enough so they bent and twist then rot
Rear panel below step - what a stupidly designed panel ... never seen anything designed to rust so fast in all my life !
rear quarters - these suffer due to blocked drain holes and also at the ends where the arches mount
Rear arch fitting area - too many pieces joined together was alwasy going to cause problems.
side sill/box section - if you make a box section out of 4 pieces and spot weld the whole lot expect it to rot
Front doors - suffer the same aas any other vehicle, blocked drain holes usually the culpret, although the seals dont help much if the water gets behind them
Windows in minibuses - inadequate rubbers cause the metal they fasten toto rot, just like the back doors, by the time you see it its usually too late
Front box section - inadequate drainage and badly designed results in water sitting in it, and phase2's have issuses with bumper mounts getting rusted solid for same reasons
Bonnet - front edge always rusts due to being twin skinned and sloping at the front, causing water to get between the skins and rot out - some drain holes would have been nice !
Inner wings/bonnet hinge area - always seems to rot, probably due to crap fitting of strengthening panel (if they will keep spot welding areas that flex the sealant will crack)
Front shock mounts (top) - is a sealed box effectively and can be prone to rusting out, not as bad as some other areas, but again some drain holes would have been nice
Front chassis legs/spring mounts -
what were they thinking, too many joints and only spotwelded was always asking for trouble
Main chassis - biggest culprets in this area is the out riggers front and back, front behind mud flaps (usually drilled to accept mud flaps) and rear behind the wheels - these are dreadful for rotting, dont bother with replacement panels, go to your local steel workshops and get some 2 or 3mm galv ones made
Floor - Front footwell over chassis, again inadequate spot welds used allowing water and damp to get between the joints, Rear - omg, how many different panels, these were designed like a jigsaw puzzle for a 5 year old
... far too many joints in an area that gets stuff loaded onto it and treated roughly, this causes the sealant to break as the panels flex, then it rots at the joints ..... this was done so they could use one floor and then change the outer edge panels depending on which variant of van it would be (twin/single etc)
Body seams - as per most vehicles with these, they suffer over time, dig out the selant they use between the panels before welding and you will usually see daylight as the panels have flexed over time - answer ... weld the bloody lot (i filled one side and welded the other as one was not as bad as the other, but i might regret that)
Towbars - these can place quite a bit of strain on the rear chassis legs, better to spread the load over a bigger area than just the bumper mounts
Windscreen area - some say this is a problem area, i guess i will find out when i remove mine, but as with any rubber seal if water gets under it, it will start to rot and you wont know, fords do seem to be rather prone to this
other than that - they last for years
Y know, when the Mk2 was still current (just)
i have even seen W and X reg with arch rust and new shapes as well! 