Hi david, self build can be a little complicated, to build any house here in portugal you require a license, part of the process to obtain a license involves registering your builder as responsible for the construction, only builders with an alvara (license to do this type of work) can register to collect the license, if you plan to build the house yourself then you would not have the license that the council require.
if you plan to build the house yourself with the help of a builder then you can register the builder using his alvara to get your license to build, you will be able then to do some of the build(technically under his name/license) and he would do some of the work too.
its a bit of a compromise but should help you move the project forward.

planning for wooden homes is pretty much the same as planning for conventional homes, it will still need all the requirments, arcitectual drawings, tech drawings, etc etc, and it will take a long time to be approved.

for more information on building a property in portugal take a look at this link
A guide on how to build a house in Portugal

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www.gekkoportugal.com A guide to living, working and buying property in Portugal