Quick question (short version):

I’m replacing loose hub ball bearings in a 25-year-old Motobecane Grand Tourer with Weinmann concave rims. The owner is lending the bike to me (sort of giving to me) as my non-beater beater city bike . It was bought to ride cross-country in the mid eighties then pretty much garage stored. Pretty good shape for its age. I rode it last season and now, as my finances do not allow me to buy a bike, I realize I’ll be on this one for at least another season or more, so I decided to do a systematic full overhaul. I’m pretty good at mechanics when I set my mind to it, with a roll cab full of tools, but with limited experience working on bikes and no bike specific tools. I plan on doing the overhaul in stages over several weeks or months.

So, last week I set out to replace the wheel bearings.
The bearings for the front hub that the grease monkey in the LBS sold me were mixed sizes (!) some noticeably smaller than others. I did not catch this until after having installed the mismatched bearings and a frustrating week of not being able to get my front hub adjusted correctly: when ever the hub was adjusted smooth without play off the bike, it became loose as hell once mounted on the bike. I’d even got some rim slap against the brake pad…I chalked this up to not having a cone wrench for precise adjustment along with some mild warp of the rim. Even so, I couldn’t understand why the wheel would be so loose. I read Sheldon and other sources before beginning, so knew what to expect. Some laziness and haste on my part for not completely stripping down the assembly are to blame. Nonetheless, I readjusted the hub countless times to the same effect. I rode about 25-30 miles with this looseness.

Finally, disgusted, a week later I started stripping down the hub. When I removed the cone I was shocked to see, instead of the bearings sitting in a grease configured ring’ (more or less), that a couple bearings were sort of partially ‘stacked’ above one another. WTF?! I dumped four bearings out and then noticed they were two different sizes!
I grabbed my Mitutoyo digital micrometer, my wheel, and headed over to the LBS. Having been sold two different size bearings was just a single element of one of the most indifferent and incompetent customer service experiences I've had in recent memory here in NYC, at the hands of this LBS. The grease monkey responsible said he’d replace the bearings in the hub for me, but now I'm somewhat regretting letting this mechanic even touch the wheel.
I'm concerned that having ridden the bike in that state may have damaged the cones or races? Anyone have an opinion based on experience?

The long version is more heinous; I just want to get some experienced mechanical feedback ASAP before I boogie over to the LBS.