It is amazing what a little clarity of vision, married with a well-defined goal, can enable one to accomplish.
It has never been lost on me that D&D is a toolkit. Especially D&D as presented in the LBBs. It is also well-known that it demands tinkering and house-ruling right out of the box (pardon the pun). I think, though, that maybe "house rules" is a term that is a bit misleading. I think the term should be "campaign modifications", or some variation thereof. Please allow me to explain.
For virtually my entire gaming "career" I have house ruled any game I have ever owned. Whether I had a group or not, a campaign in development or underway, or not, I was house ruling. It never dawned on me that I wasn't house ruling at all. Without a campaign in mind, I was actually modifying the toolkit. It isn't until the toolkit is applied to the campaign that it becomes a rules set. Some changes can be made to the toolkit, to be sure. The vast majority of the house rules should be informed by specific details of the campaign, however. Very few people will go to their workshop and modify their hammer or screwdriver, but they will take the blueprint for a project and modify it to better suit the unique nature of their needs.
Development of Dannak has lead me to this conclusion. Anyone can play D&D straight from the box. Anyone can start house ruling willy-nilly on their first read-thru. The best modifications, though, are the ones implemented to reflect specific peculiarities of the campaign.