Magento – Update Product Prices and Images Using SQL Query

Let's say that $storeId is the store for which you want to update the price $specialPrice is your special price, $sku is your product SKU, $fromDate and $toDate are...well, you get the idea.

Now run this code:

$id = Mage::getSingleton('catalog/product')->getIdBySku($sku);
if ($id) {
    Mage::getSingleton('catalog/product_action')->updateAttributes(
        array($id), //array with ids to update
        array( //array with attributes to update
            'special_price' => $specialPrice,
            'special_from_date' => $fromDate,
            'special_to_date' => $toDate,
        ),
        $storeId //store id to update. If you want to update the global value use 0 in here
    );
}

I don't think that using the SOAP services will get you what you need fast. I mean it will probably work, but it will be really slow for 3k products.
Instead try this script.
Let's say that your csv has 2 columns. SKU and price.

$skuIndex = 0;
$priceIndex = 1;
$csv = 'path/to/file.csv';
$io = new Varien_Io_File();
//an array to keep the products by price
$productIdsByPrice = array();
//a product model instance
$productModel = Mage::getSingleton('catalog/product');
//read the csv
$io->streamOpen($csv, 'r+');
while($csvData = $io->streamReadCsv()){
   if (count($csvData) < 2) { //skip rows with less than 2 columns
       continue;
   }
   $sku = trim($csvData[$skuIndex]);
   //get the product id by sku
   $id = $productModel->getIdBySku($sku);
   if ($id) {
      //if the id exists then mark it for update
      $price = trim($csvData[$priceIndex]);
      if (!isset($productIdsByPrice[$price])) {
         $productIdsByPrice[$price] = array();
      }
      $productIdsByPrice[$price][] = $id;
   }
}
//now you should have the product ids you need to update grouped by price
//just do the fast update
foreach ($productIdsByPrice as $price => $ids) {
    Mage::getSingleton('catalog/product_action')->updateAttributes(
        $ids, //what products to update
        array('price' => $price), //what attributes to update
        0 //store id for update
    )
}

you can place this code in one of your custom models or helpers and then run it. You may want to double check the code. I haven't tested it. Also backup your db.

[EDIT]

If you run this from a file, create one called price_update.php on the same level as index.php and add this in it:

<?php 
error_reporting(E_ALL | E_STRICT);
define('MAGENTO_ROOT', getcwd()); 
$mageFilename = MAGENTO_ROOT . '/app/Mage.php'; 
require_once $mageFilename; 
Mage::setIsDeveloperMode(true); 
ini_set('display_errors', 1);
umask(0);
Mage::app();

After this, add the code from above that parses the csv and call in your browser MAGE_ROOT/price_update.php.