Since you have a goal of working toward scratch building, I'd recommend a [nearly] all balsa kit -- as opposed to one with cut plywood fuselage parts.

I say that because in scratch building you will need to deal with fitting and aligning fuselage parts. Unfortunately, a plane like a SIG Kadet LT-40 or a Goldberg Eagle will be an outstanding trainer with the highest probability of building true because they use alignment techniques that are not very practical for scratch building and materials that are not the best for scratch building... so they really do little to teach you about building fuselages other than show you what a good one looks like once it's built.

As for wing construction -- egg-crates such as found in the PT-40 Mark-<whatever's newest> will similarly deprive you of the learning experience in the wing department.

The skills you'll need include shaping and fitting parts (shaping can be a little creative, but fitting should to be pretty precise); aligning similarly shaped parts (pretty precisely with or without tab-and-slot aligners); ad libbing (i.e. engineering on the fly for things like installing control systems that plans tend not to define too closely where kits often define things very rigidly in advance).

In today's market, you're not too likely to find a trainer that's great for both teaching you to fly and teaching you to build, but something in-between should be available with some of the benefits for both skills. Or, if you make friends with a rabid builder real quick, you could get them to coach you through a scratch-built project. There are a lot of good trainer plans out there.