You can make it so that the PayPal button is not on the checkout page at all by putting in some extra code on your checkout page.
On this page the PayPal button code starts on line 591 through line 600. You can add in this code around the PayPal button to stop it from showing:
<?php
if($WAGLOBAL_Gateway == 1 ) { //Check your setting in the WA_Globals to ensure you are using the correct gateway
?>
the PayPal button code should be inside of this code
<?php } ?>
So the original code should look like this:
<?php if(!WA_Auth_RulePasses("No Payment Gateway")){ // Begin Show Region ?>
<div class="checkoutHeader">Fast, Secure Checkout with PayPal</div>
<div class="contentBox">
<form name="PayPal_ExpressCheckout_form" action="<?php echo $_SERVER["PHP_SELF"]; ?>" method="post">
<p><input type="image" alt="PayPal Express Checkout" name="PayPal_ExpressCheckout_button" id="PayPal_ExpressCheckout_button" src="WA_eCart/PP_ECO_Scripts/btn_xpressCheckoutsm.gif" />
<p>Save time. Checkout securely.<br />Pay without sharing your financial information.</p>
</form>
</div>
<br />
<?php } ?>
You will want to update it to be this instead:
<?php
if($WAGLOBAL_Gateway == 1 ) { //Check your setting in the WA_Globals to ensure you are using the correct gateway
?>
<?php if(!WA_Auth_RulePasses("No Payment Gateway")){ // Begin Show Region ?>
<div class="checkoutHeader">Fast, Secure Checkout with PayPal</div>
<div class="contentBox">
<form name="PayPal_ExpressCheckout_form" action="<?php echo $_SERVER["PHP_SELF"]; ?>" method="post">
<p><input type="image" alt="PayPal Express Checkout" name="PayPal_ExpressCheckout_button" id="PayPal_ExpressCheckout_button" src="WA_eCart/PP_ECO_Scripts/btn_xpressCheckoutsm.gif" />
<p>Save time. Checkout securely.<br />Pay without sharing your financial information.</p>
</form>
</div>
<br />
<?php } ?>
<?php } ?>
As for altering the user login portion this is a built in part of the PowerStore that is relied on further in the process. Removing this functionality can be difficult and will require some custom coding beyond just removing it from the checkout page.