[Sony Ericsson Xperia Mini, Mini Pro, Xperia Pro, A] Ticklefish:
It's not your stamina mode icon and alarm icons that are beside the clock..it's your status icons. And one look at your code told me instantly where they're there..

<?xml version="1.0" encoding="utf-8"?>
<com.android.systemui.statusbar.phone.PhoneStatusBarView android:orientation="vertical" android:background="@drawable/status_bar_background" android:focusable="true" android:descendantFocusability="afterDescendants"
xmlns:android="http://schemas.android.com/apk/res/android"
xmlns:systemui="http://schemas.android.com/apk/res/com.android.systemui">
<LinearLayout android:orientation="horizontal" android:id="@id/icons" android:paddingLeft="6.0dip" android:paddingRight="6.0dip" android:layout_width="fill_parent" android:layout_height="fill_parent">
[COLOR="DarkOrange"]	<LinearLayout android:id="@+id/statusbarleftside" android:orientation="horizontal" android:layout_width="fill_parent" android:layout_height="fill_parent" android:layout_weight="1.0">
[/COLOR]	<com.android.systemui.statusbar.StatusBarIconView android:id="@id/moreIcon" android:visibility="gone" android:layout_width="@dimen/status_bar_icon_size" android:layout_height="fill_parent" android:src="@drawable/stat_notify_more" />
<com.android.systemui.statusbar.phone.IconPartitioner android:layout_width="0.0dip" android:layout_height="fill_parent" android:layout_weight="1.0">
<com.android.systemui.statusbar.phone.IconMerger android:gravity="center_vertical" android:orientation="horizontal" android:id="@id/notificationIcons" android:layout_width="wrap_content" android:layout_height="fill_parent" />
[COLOR="Red"] <LinearLayout android:gravity="center_vertical" android:orientation="horizontal" android:id="@id/statusIcons" android:layout_width="wrap_content" android:layout_height="fill_parent" />
[/COLOR] </com.android.systemui.statusbar.phone.IconPartitioner>
[COLOR="DarkOrange"]	</LinearLayout>
[/COLOR]	<com.android.systemui.statusbar.policy.Clock android:textAppearance="@style/TextAppearance.StatusBar.Clock" android:gravity="left|center" android:id="@id/clock" android:paddingLeft="6.0dip" android:layout_width="wrap_content" android:layout_height="fill_parent" android:singleLine="true" />
<RelativeLayout android:id="@+id/statusbarrightside" android:layout_width="fill_parent" android:layout_height="fill_parent" android:layout_weight="1.0">
<LinearLayout android:id="@+id/statusbarinsiderightside" android:orientation="horizontal" android:layout_width="wrap_content" android:layout_height="fill_parent" android:layout_alignParentRight="true">
<LinearLayout android:gravity="center" android:orientation="horizontal" android:id="@id/signal_battery_cluster" android:paddingLeft="2.0dip" android:layout_width="wrap_content" android:layout_height="fill_parent">
<include android:id="@id/signal_cluster" android:layout_width="wrap_content" android:layout_height="wrap_content" layout="@layout/signal_cluster_view" />
<TextView android:layout_gravity="left|center" android:id="@id/battery_text" android:paddingLeft="4.0dip" android:layout_width="wrap_content" android:layout_height="wrap_content" android:text="@string/status_bar_settings_settings_button" android:singleLine="true" style="@style/StatusBarNotificationText" />
<ImageView android:id="@id/battery" android:paddingLeft="4.0dip" android:layout_width="wrap_content" android:layout_height="wrap_content" />
</LinearLayout>
<ImageView android:layout_gravity="center_vertical" android:id="@id/stat_no_sim" android:background="@drawable/stat_sys_no_sim" android:paddingLeft="4.0dip" android:visibility="gone" android:layout_width="wrap_content" android:layout_height="wrap_content" />
</LinearLayout>
</RelativeLayout>
</LinearLayout>
<LinearLayout android:orientation="horizontal" android:id="@id/ticker" android:paddingLeft="6.0dip" android:animationCache="false" android:layout_width="fill_parent" android:layout_height="fill_parent">
<ImageSwitcher android:id="@id/tickerIcon" android:layout_width="@dimen/status_bar_icon_size" android:layout_height="@dimen/status_bar_icon_size" android:layout_marginRight="4.0dip">
<com.android.systemui.statusbar.AnimatedImageView android:layout_width="@dimen/status_bar_icon_size" android:layout_height="@dimen/status_bar_icon_size" android:scaleType="center" />
<com.android.systemui.statusbar.AnimatedImageView android:layout_width="@dimen/status_bar_icon_size" android:layout_height="@dimen/status_bar_icon_size" android:scaleType="center" />
</ImageSwitcher>
<com.android.systemui.statusbar.phone.TickerView android:id="@id/tickerText" android:paddingTop="2.0dip" android:paddingRight="10.0dip" android:layout_width="0.0dip" android:layout_height="wrap_content" android:layout_weight="1.0">
<TextView android:textAppearance="@style/TextAppearance.StatusBar.PhoneTicker" android:layout_width="fill_parent" android:layout_height="wrap_content" android:singleLine="true" />
<TextView android:textAppearance="@style/TextAppearance.StatusBar.PhoneTicker" android:layout_width="fill_parent" android:layout_height="wrap_content" android:singleLine="true" />
</com.android.systemui.statusbar.phone.TickerView>
</LinearLayout>
</com.android.systemui.statusbar.phone.PhoneStatusBarView>

Do you spot the line in red? And do you spot which LinearLayout it's in...? ;)