I'd go with a Sig 4-Star 40 kit. Straightforward build, meets your low wing requirement, and is fairly easy to fly, capable of advanced performance (aerobatics) and makes a good second plane. It doesn't have retracts, but I'd save that for a 3rd or 4th plane. It doesn't have flaps either, but if you really wanted them, it wouldn't be difficult to convert a part of the strip ailerons to a flap, it would require an additional servo and the linkage, though.

As far as tools go, that is a question if you ask 30 different people will give you 40 different answers.

VERY basics:
1-flat building surface
2-straightedges (good foot ruler and a metal yardstick), and a small square or draftsman's triangles
3-exacto knife and #11 blades OR single-edge razor blades
4- good pair of scissors
5-razor saw
6-medium size pair of pliers and /or vise-grips
7-small and medium tip screwdrivers, straight and phillips
8-pair of forceps
9-T-pins, wax paper
10- small clamps to hold parts after gluing
10-1/2-and I'm sure there's a thousand more things

I think there's a "sticky" on one of these threads with the most popular things to have