When you click on links to various merchants on this site and make a purchase, this can result in this site earning a commission. Affiliate programs and affiliations include, but are not limited to, the eBay Partner Network.
The major change was mid 06 they went to the "commonized" heads which is easily identified by the yellow round engine oil dipstick vs the old black T-handle. Changeover was December 05/January 06. Not a long production run at they stopped selling the 6.0 at the end of 2006 in the truck. The vans did continue all the way to 2010 without any further changes. The general consensus is the commonized heads have some additional strength to help deal with head gasket issues but I haven't seen any hard testing to actually back that up.
There were some other minor changes to the wiring harnesses and the 07's got a groove added to the turbo to help with unison ring sticking issues.
None of these are deal breakers and I have no issue recommending an 05 or early 06 so long as the buyer is aware of the potential issues. I generally prefer those to the 03/04 as you get the better high pressure pump and front suspension/higher GVWR ratings.
I think the turbo changes in 2006 were good (also included the larger drain tube), and also the commonization changes (Jan 11 '06 production date and later) were good.
I didn't like the changes back and forth with the MAF sensor in 2005. There were some other "mid-year" changes in 2005 that were good.
The failure prone HPOP STC fitting never got updated in the F-series, but my understanding was that it did get updated in the 08 E-series.
2007 model year engines did receive a revised oil drain passage in the turbocharger to further improve reliability.
I think the turbo changes in 2006 were good (also included the larger drain tube), and also the commonization changes were good.
Not sure when the oil drain tube update took place or if it coincided with commonization or not, but my 2006 had the old drain tube and is precommonized. It also had the old flexible oil feed tube. Recently replaced both while doing a bunch of stuff to it.