I just reviewed them quickly and there is nothing about torque specs or torquing order. Nothing about alignment dowels. The list of required tools does not even include a torque wrench.
Nothing about aligning the bellhousing. Nothing about using an alignment tool.
Additionally the author recommends greasing the pilot bearing however these bearings come pre-greased.
Sorry to be the bearer of bad news but IMHO an individual who is not a professional mechaninthat can change his own clutch on a 99+ Mustang is very rare.
The instructions above pretty much describe the order, but clearly is not a very quality write up. It would take me a good 1/2hr to describe the entire process in detail. If you have NO basic idea of what this job requires and are very uncomfortable in doing the job, take it to someone and pay to have it done. If you do have the basics down and feel you have the tools and are capable, I'll try to provide some info that may help you.
What needs removed (roughly in this order): Shifter, H or X pipe, Driveshaft (its a 12mm 12pt, the write up linked above didnt know), starter, transmission crossmember, disconnect clutch cable, and electrical connectors. Before anything, disconnect the battery or you're gonna get sparks when you try and remove the starter. Shifter handle should be done first with the trans in neutral.
If I remember correctly, ALL sizes are metric except the small bolt that holds the dust cover for the clutch cable, thats 1/4". If you can get a hold of a driveshaft yoke, you can save yourself from draining the trans fluid IF its in good shape by plugging it in the back of the trans when you pull the driveshaft out.
For the clutch, just remember to have a clutch alignment tool. If its not aligned, you will have problems. IMO the only torque specs you really NEED to pay attention to is for the flywheel and the clutch pressure plate bolts. Be sure to get the correct tightening order as well. You should replace the flywheel or have it resurfaced as well. I actually didnt do this myself when I did my own clutch, but well over 30k miles and I've never had any problems. I DO NOT recommend you do this though.
I hope this info helps. If none of this makes sense, have someone else do it. You dont want to be halfway through and realize you're in over your head.