Hi,
2 questions:
1) How much does it cost to register a tourist visa (after 30 days)?
2) Do I have to get a permit in order to cross through the pamirs from Tajikistan to Kirgizstan?

It depends on where you will apply for the Visa.
I applied Tajikistan Visa in Baku, Azerbaijan and it was US $30 this summer but they didnot issue GBAO permit. I applied for GBAO permit in Uzbekistan and I had to pay US$20. I heard some one told me it was free 4 days ago. Other traveller pay US$60 or $70 for Visa and permit in Tashkent.

Not sure if you are asking about visa or ovir registration. I assume the latter and that you haven't already got registered, in which case you are in for a fine of undetermined amount if you stay beyond the 30 days.
I would recommend trying to deal with the fine in a large town or Dushanbe rather than at the border where they have you at their mercy!