Question 1:
Answer: go to start, run, type msconfig, press ok, go to boot.ini and click on check all boot paths and it should/will remove the invalid ini file.
Question 2:
Answer: Since we cleaned up your system, does IE still do this? If so, try uninstalling it and reinstalling via add/remove, add/remove windows components in the control panel.
Question 3:
Answer: You more than likely will never see 56k, your dial up will vary almost everytime you connect, it also depends on the traffic on the line, how long the line it, how old it is, etc. There are a lot of factors that determine this.