What hypo said. I'm not that familiar with XD-E but had XF for years. Apart from the coils on the XE, it also has the advantage that the boot can take a full size esky, which I don't think the XD could and still shut the lid.
Re the auto/manual swap, go to http://ford.i8.com/discuss.htm
and go back through the topics until you find one (I think there might be two separate threads a bit of time apart) about auto to manual conversion by Bass Crazy. It's EA, but the general operation will be similar although the details are different. I think it took about four blokes about ?16 hours to swap the manual into an auto and vice versa. I've pulled gearbox off XF to do clutch and I think it's maybe half a day out and in, and dash out and replace pedal box on EA was about 6 hours but you could do it in half the time if you don't stuff around like I did. I don't think 2 blokes with general mechanical skills would have any trouble converting auto to manual in a weekend, maybe a lot less.
On dropping the manual box, remove the gearshift lever BEFORE dropping the box. I made the mistake of following the destructions in the workshop manual and after dropping the box part way and attempting to remove the lever as instructed I found that the bloody thing was an XD-E type which I couldn't budge or get at to remove. This was a huge help as I couldn't get the bastard back in at the clutch end or move it in any direction. So I forced it out with a pry bar and broke the fork. It was that or cut the bloody lever.
Watch the firewall on the XD-E-F as it's not strong enough for manual and will flex and eventually pull through if it's not reinforced. A plate on the firewall side can be held on by a few self tappers as the clutch cable adjuster holds it in place any way. Swap the clutch cable tube and plate that should be on the manual donor into the XE to get the right angle on the cable and a bit more reinforcement. Or do yourself a favour and convert it to hydraulic at the same time.
If the earlier dashes are anything like the E series, get the workshop manual as the order of work isn't the way you'd approach it naturally.
Others will know the other stuff.