Be sure you trace all the bits and pieces that aren't shown explicitly on the plans if you want to build another when you're done! I'm pretty sure my LT-25 plan doesn't show what all the pieces look like, since they are all pre-cut for you.

I'm planning to do the same thing except it's because I want to learn fly with the stock wing, but then play around with flaps once I'm starting to get the hang of this flying thing .

If you get a used engine, then I suspect you can stay under $400 without too much trouble, especially if you already have some of the building supplies. I'm sure all the odds and ends end up costing a bundle, but just looking at the major items... $70 for a kit (my LT-25 was $67 at tower hobbies), $130 for a 4-channel radio with 4 servos, even a new OS 25LA or magnum xl-25 is only about $60 (and shoot, the 40LA looks to be the same price as the 25LA if you are a member of the "more power!! HARHARHAR" camp). That should leave over $200 of your initial $400 for other bits and accessories... I priced out a full set of building materials from tower once (one of each CA, one of each epoxy, the fancy aluminum sanding blocks and a bunch of several grits of sticky-back sandpaper, razor saw, xacto knife etc.) and it was ~$100
That leaves another $100 for flightline supplies.

I think if you're careful, you should be able to come in under $400 easily.

-Rick