GPX format is always in
EPSG:4326, so nothing wrong about that.
If the orthophotos are correctly georeferenced, it should be no problem to add them to the project. Make sure you choose the right CRS for that layer, and enable on-the-fly-reporjection under
Settings -> Project settings. It does not have to be the same CRS as the GPX layer is.
You can add Openlayers plugin and Google or bing satellite imagery to see if your layers are in the right position. For that plugin, the project CRS must be
EPSG:3857. The layers can still have other CRS.
If your orthophotos are correctly georeferenced, they should line up with the satellite imagery. If they do not, you can use the georeferencer to re-georeference them by referencing with points on the satellite background.
To export your waypoints as shapefile, rightclick on the layer and
Save As ... You can even select another CRS in that step.