I believe you need to make your switch happen way sooner then you are, right after $app is checked for. Also, try converting the prices, and also testing that you have what you expect. Here are some things to get you rolling.

Convert Price from Current Currency to Base Currency and vice-versa

<?php
$baseCurrencyCode = Mage::app()->getStore()->getBaseCurrencyCode();
$currentCurrencyCode = Mage::app()->getStore()->getCurrentCurrencyCode();
$price = 100;

// convert price from current currency to base currency
$priceOne = Mage::helper('directory')->currencyConvert($price, $currentCurrencyCode, $baseCurrencyCode); 

// convert price from base currency to current currency
$priceTwo = Mage::helper('directory')->currencyConvert($price, $baseCurrencyCode, $currentCurrencyCode);
?>

Changing price from any one currency to another

<?php
$from = 'USD';
$to = 'NPR';
$price = 10;

$newPrice = Mage::helper('directory')->currencyConvert($price, $from, $to);
?>

Get Currency Rates

<?php
/**
 * Get the base currency
 */
$baseCurrencyCode = Mage::app()->getBaseCurrencyCode();

/**
 * Get all allowed currencies
 * returns array of allowed currency codes
 */
$allowedCurrencies = Mage::getModel('directory/currency')->getConfigAllowCurrencies();

/**
 * Get the currency rates
 * returns array with key as currency code and value as currency rate
 */
$currencyRates = Mage::getModel('directory/currency')->getCurrencyRates($baseCurrencyCode, array_values($allowedCurrencies));

$allowedCurrencies = Mage::getModel('directory/currency')->getConfigAllowCurrencies();

/**
 * Get currency rates for Nepalese Currency
 */
$currencyRates = Mage::getModel('directory/currency')->getCurrencyRates('NPR', array_values($allowedCurrencies));
?>

I will paraphrase the answer of St0iK. You can't set different base currency per store, but you can do it per website. First you have to go to the admin panel -> System -> Configuration -> CATALOG -> Catalog -> Price -> Catalog Price Scope and change it from Global to Website. Now when you go to the admin panel -> System -> Configuration -> GENERAL -> Currency Setup -> Currency Options you can change Base Currency per Website, not only for Default (Global). So you have to transfer you stores to websites and you will be able to do what you want.