I ran a HORSE tourney for my birthday a long time ago and asked for advice. You can see the thread here:
http://www.chiptalk.net/forum/tourna...ighlight=horse
The blind schedule for the 50 000 HORSE tourney at the WSOP can be found by clicking on the link on this page (I found this useful)
http://www.worldseriesofpoker.com/ev...?eventid=36507
Essentially we switched games each orbit (as opposed to time, which is also possible) and the stud-based games had no blinds. Since it was an orbit based thing, no one had to pay more/less than others.
The thing that was the most weird for me was that it was limit, which meant the tourney took FOREVER, especially with all the split pot games. Doing a pot-limit/NL mix would probably be better... and I like your idea of substituing in Pineapple.
Hope this helps,
lucky.