Hi Chris - welcome
If I were in your shoes I would probably go for a 2.0 110, as it is the most economical, and the best all-rounder for driving - it can also be remapped to 140bhp which is more than a standard 2.2Hdi. There are no FAPs to worry about, the vacuum system is simpler and it has a standard flywheel so long term maintenance is easier/cheaper.
The 2.0 90 is a cracking little car and the most robust engine choice, but its less economical than the 110 as it has to work a bit harder on journeys, and it take a while to get it up to speed....
I have a 2.2Hdi, as do a few of us here, which can suffer from vacuum issues, FAP issues and less MPG, but once these issues have been remedied ( VW anyone? ) then its a cracking car with a good 160bhp while still getting 40mpg round town and 55mpg on a run.
Both the 2.0 and the 2.2 are basically the same block/layout, so not much between them for working on.
As for buying a second hand one - the 2.2Hdi seems to fetch a lower price than the 110 due to the fear factor, which will work in your favour once sorted - there are loads of 406 estates on tinterweb, try to find one with good history, not necessarily low mileage as these cars can last a long time. An ex private hire 406 was recently sold that had covered over 448,000 miles.
Try also to get a GLX or higher spec, as the price difference between these and the lower spec LX's is negligible, but the GLX can be retrofitted with cruise, leather etc should you wish.
Here is a small selection of whats availble at the moment;
http://www.ebay.co.uk/itm/221894486088? ... EBIDX%3AIT
http://www.ebay.co.uk/itm/2003-PEUGEOT- ... 2358c0e457
http://www.ebay.co.uk/itm/2002-PEUGEOT- ... 464189b91b
http://www.ebay.co.uk/itm/2003-PEUGEOT- ... 2102ebcd85
Kelv.