Input Field Appearance

Your stylesheet (beginning at line 935) sets rules for different input types

[css]
input[type=text],
input[type=password],
input.text,
input.title,
textarea, select {
	font-size: 1em;
	margin-top: .5em;
	margin-bottom: .5em;
}
input[type=text],
input[type=password],
input.text,
input.title,
textarea {
	background-color: #FFFFFF;
	border: 1px solid #999999;
	padding: 5px;
}
input[type=text]:focus,
input[type=password]:focus,
input.text:focus,
input.title:focus,
textarea:focus {
	border-color: #666666;
}
textarea {
	width: 30em;
	height: 20em;
}

You're using the HTML5 enabled fields and your email field is type="email" - that's not defined in your CSS along with the other types. If you add that to your rules, then everything should format the same. Since you're using the HTML5 fields, you'll probably want to add the "tel" and "url" types as well for the phone and website fields.

[css]
input[type=text],
input[type=email],
input[type=password],
input[type=url],
input[type=tel] {your:styles}

Never edit/change the Gravity Forms files in it's plugin folder as your changes will be overwritten whenever an automatic update is run.

You always place customizations in your theme or child theme files. CSS customizations would go in your themes stylesheet, code customizations using hooks/filters would go in your themes functions.php file.