subedikancha,

1.) does  USCIS charge for the amendment petition after the H1B approval to get the H1-I -94?

Yes. The fees for an amended I-129 petition for COS should be same as the original.

2) which one is better to show USCIS while filing H1B to maintain the status till october( with the ESL I-20 or Kaplan I-20) since I am filing under Master's Degree quota(MBA)?

Shouldn't matter to USCIS which school you go as long as you have a valid I-20 and you are in status. Come to think of it, they'll know what you are doing (that you are just bridging the gap) but won't have any ground to deny your petition, provided you have proper documents.

USCIS knows that this Gap is a problem and in 2004, they had actually allowed to stay without any new visa status or F1 extension even if you had a gap. Unfortunately this cap gap relief they provided was discontinued after 2005. So don't worry about USCIS, they know what's going on.

3)  Since Kaplan issues I-20 only for 6 months and if they issue I-20 now, its going to expire before sept 31 and I again need to maintain status till oct 1st ,what is yr suggesstion on that?

I don't know much about Kaplan. As for ESL, you can get an I-20 for upto 12-16 months I think. Getting an I-20 for 2 levels (about 8 months) should do the trick.

(P.S: Do not take anything explained here as legal advice and discuss all the options with your lawyer.)