2nd SSD as main boot disk, what do I do with old filesystem?

Hello StackExchange!

After a couple years of using my macbook pro, performance has deteriorated with each update to OSX. I've tried a few things to improve it, and with no results, I decided to get a 128G SSD and a drive caddy for the CD drive, and install a clean install on it.

Using the SSD as my main boot drive, and wahla, great experience. Now, I just need my old stuff. Migration assistant isn't ideal because:

A) the SSD is 128G, and the HDD is 500G. Lots of applications.

B) I don't want to blindly copy over batches of filesystems, mostly because it's likely that I will copy over whatever caused performance deterioration in the first place (most likely my tinkering).

So, my questions are:

What's the best way to access and organize the files and applications on my HDD?

Can I just copy over specific applications? How do I copy their settings?

Are there things I should remove from the HDD? Like the old User Account?

Thanks in advance.