Yeah you shouldn't have replaced the motherboard first, should have tried the HDD. Try restoring the ipod first. After you have done that, if the ipod is making clicking noises when it freezes, you know it is the hard drive. I had this problem with my ipod 3g 30gig two years ago. Then I looked up ipod hard drive problems, and found that banging your ipod will fix the hard drive. I took mine apart, cleaned the zif connectors and put them back in, and it still froze. So I banged my ipod about 14 times against my palm, and It fixed the freezing! I have had my ipod working for two years, and I installed an iVue clear panel and leds into it. So before you buy another hard drive, you might want to try that fix method first.
http://www.wikihow.com/Fix-a-Broken-iPod