Clunk in front-end

Hey. So I drive a 95 Mazda Protege ES. I purchased the car about a year and a half ago and have put my share of work/cash into it (not a complaint, I love my little car) When I bought it I knew my struts were bad. I didn't have the time or money until recently to replace them. But they did get replaced and I got an alignment the same day. Well, about a week before I did all 4 struts I noticed a clunking sound going over bumps. (Before I got around to doing the struts I learned my axles were bad) So I figured the clunk was from the bad axles. Boots were torn, grease everywhere, noises and just very annoying. So I fix my struts about a month ago. 2 weeks ago I start hearing this flapping sound on my front right tire. Almost like when you were a kid and would tape a playing card to your spokes on your bicycle so when you would take off you'd get that whirling noise? It sounds similar to that. Anyways, I repaired both axles last night. Everything went well for the initial road test after the work completed but now all day today the sound is still there. Also to note: the whirling or flapping sound only happens in 1st and 2nd gear. Once I shift into 3rd it goes away completely so it's only at lower speeds. Also, when I brake you hear a "grinding/rubbing" sound. Again, I assumed it was my faulty axles. But, even after axles and struts it's still there. The car feels fine (I don't notice any differences, major or minor) but it is highly irritating not knowing the source and cause of this sound. Also sometimes when I brake and am coming to a stop (I'd say between 15-0 mph) my brakes squeel but I have new pads and rotors. Rotors and pads were done about a yr ago and pads were done again when I did the struts. If anyone has any suggestions please reply, as I'm anxious to get this fixed.