This issue has come and gone over the years with different fixes along the way, so here is my updated guide to this issue as of this date January 5th, 2016.
Check the EDIT section below, there is a much faster way to fully update Windows 7 SP1 after a clean install now.
This is what I do when I reinstall Windows 7 with SP1 or have issues with Windows update stuck on checking for updates.
If Service Pack 1 is not installed, install it before following this guide.
for 64bit W7 or
for 32bit W7
Download KB-3138612 and save it where you can find it later
Download SUR Tool save it to same place
Restart the PC and disconnect from internet before Windows loads, this is important because at every boot windows will check for updates in the background and this will start the checking for updates hang all over again and will prevent the install of the downloaded packages until it finishes checking, so disconnecting from the internet before Windows loads prevents this.
Once booted install KB-3138612, if reboot is required do so and stay disconnected from internet.
Now install the SUR Tool package, this is a big package and will install many updates along with cleaning up and repairing the Windows update store. It will also cut down on how many more Windows updates will need to be installed later.
After install of SUR package reboot, connect to internet and do a manual Windows Update, it should work much faster now. Even after these fixes I have seen some W7 PC's take up to an hour to finish checking for updates if launched from Control Panel manually.
If you have other Windows updates issues and the 2 updates above are installed, download this Microsoft Windows Update fixit tool (right click "save link as") run it and select aggressive mode to completely reset Windows updates. Reboot and try Windows Updates from the Control Panel again.
Update: Microsoft has released a huge update rollup for Windows 7 SP1, this is similar to a service pack but they are not calling it that. This will make it Much faster to update Windows 7 after a clean install, no more Windows update issues and many reboots. This update rollup will bring the system current to patch Tuesday of April 2016.
This is not being released through Windows Update, you have to use Internet Explorer to get it, open IE and go to this address
Type in the search box 3125574 and hit enter key.
Now you will see all versions of this rollup, select the one you need and download it somewhere you can find it later. Also use the Windows Update Catalog page to download and install this update first, 3020369, it is a pre-requisite for the rollup, then install 3125574, also be sure to be disconnected from the internet when applying these updates.