First thing you need to know is any time you pull the drive off or install a drive is to have hte gear shifter in the full fwd position, this aligns the shift cable end with teh shift arm that turns the shift shaft in the bell, that turns the shift shaft in the lower unit(lots of shafts). the point where the shift shaft in the bell and the shift shaft in the lower, connect, the coupler must be pointed fwd, this will happen when hte shift cabel adn the lower unit are both in fwd position.
Second thing, check your engine alignment, most shops will rent you the tool to check it. Worse comes to worse, after you read the next step, you will have a spare input shaft that you can use to check aligment. It should slide in, engaging all the splines. Look at teh grease left on the splines to gauge which way the engine will have to change. Check it in more than one engine rotation position.
Third, the drive shaft on your Alpha is too long to replace the straigt 6 drive. Compare the input shaft lengths, you'll see the Alpha one is longer( they standardized them when they designed the Alpha). You just need to remove the end yoke(the splined end) by dissasembling the u-joint, be carefull and you can resue the u-joint if the rollers and trunions are in good shape. Just remove the c clips, tap the yoke o one side so the u-joint cup comes out, repeat the process for the other side. This is where you end having a spare yoke
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