You've got it. Practice, Practice, Practice. If I'm correct, it looks like you got a delta mortise jig? Same thing I have for my drill press. As far as the alignment, the best way is like you said, just draw the lines to the area you are mortising. I would also clamp a strait feather board on to keep the wood I am working with straight on alignment. The problem isn't so much making the mortise as it is the tenons. How are you making the tenons? Are you using a dado set or do you have a tenoning jig? I do not have a tenoning jig, which means I used my dado set and it takes a lot of patience and adjustments. I very rarely get my tenon right on with the mortise. I am usually off by a few 32nds. Which means I am sanding too. I don't want to pay the $150 for a tenon jig, but I did buy a book on making jigs and it has a way to make your own tenoning jig. Anyways, I am getting off track. What you need is a good way to make the tenons. Either buy a tenon jig or make one. Using a dado set like I have done is not an exact science. I hope this helps you some...
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