Are you going to do the work yourself or have it done by someone such as marine service shop?
If you haven't done so yet, it's important to grease up the engine coupler every year or two. There should be two ways to add grease to the coupler on your 2006 engine model....One is there should be one or two grease zerk fittings at the coupler so you can pump in max of 10 pumps. (5-6) should do it as you don't want to over fill the coupler as it gets messy and slings the grease all around when ran....The other way they grease the coupler is to add some grease on the alignment bar a few times and run the bar in and along with a few turns then check your alignment marks as needed.
Here's a look at your coupler, http://www.ebay.com/sch/i.html?_fro...313.TR1.TRC0.A0.H0.TRS0&_nkw=18643A5&_sacat=0
Here's an online manual that would help inform you of when you should be checking things over service wise along with some detailed info of how to go about it all if you have the time to read the sections that best pertain to the areas you'd need for doing the jobs.
There are also many videos of how to remove the Alpha drive, check engine alignment, U-joints, grease the gimbal bearing, inspect all the items needed, reinstall new bell housing gasket, related O-rings and stern drive.
Don't forget to put the stern drive/shifter handle in full forward gear plus remove the speedohose connector or you'll cause some damage upon removal.
Member achris of iboats has done a few how to videos that help make it easier on you + there are many others available online with a google search.
The second link below is the video by Chris found in the MUST HAVE Technical Information for DIYers.
Here's a parts catalog for your stern drive parts, http://www.mercruiserparts.com/selectSerailRange.asp?doc_nbr=ALPHA+ONE+(GEN.II)++++1998+AND+UP
Being an 2006, if you haven't yet, it's getting within the time frame to also install a new rubber water pump impeller as these style pumps are good for awhile if used under non harsh conditions. It's located between the upper and lower units of the stern drive. Merc makes a impeller kit plus you'll need about 2 quarts of Merc stern drive oil. 3 qts would be best if you don't already have some onboard the boat.
You can find alignment bars as low as $30.00 and higher depending on how many other tools you may want to accumulate that would pertain to other service work within the stern drive/gimbal housing area inside eBay, http://www.ebay.com/sch/i.html?_nkw=mercruiser+alignment+tool