How much power do you plan to throw at it? Do you really need 9" ends? Do you plan on drag racing competitively?
All questions I asked before I cut up my 8.8. I did a ton of research on the subject, I probably spent 10-15 just scouring the internet on how people shorten them. In the end, I took a $125 complete axle from the yard, cut it with a sawzall and welded it back together. It made a trip from Charleston, SC to Atlanta, GA and back with zero issues. I probably have close to 3000 mi. on it over the summer.
I measured more than a few times, scribed the tube for alignment and then cut out the measured difference between the 2 factory axles just before it tapers down on the end. I was able to jig it back in place with multiple pieces of angle iron and some hose clamps.
You can't take enough out of the driver's side on the end, you will hit the taper before you get to the ~ 2 13/16" mark you need to remove. I cut right after the taper on the end and beveled the cut for welding. Drilling out the plugs is only part of the process, you still need to remove the tube, cut it and then put it back into the housing. I read somewhere that the ends are tapered slightly to allow them to be pressed into the housing at which point I decided against it. Might have been folklore, but I knew I could cut and weld it, pressing it back into the housing would have been much much harder.
As far as 9" ends, I figured I could always add them later should I choose to, or even a c-clip elim kit. I only go to the track for fun and the tech inspection is non-existent. For test and tune they should have no issues with a c-clip rear axle. With the 300 ft lb. the engine currently makes, I am confident in the rear holding the power and the unknown mileage trac-lok is working as designed.
I guess in the end, my message is, don't over think it. Measure, measure, measure, cut, and weld. If you take your time, it will turn out fine and you will have a reliable, strong rear axle.
One thing I will suggest, remove the center pin bolt in the yard. It will save you the trouble of buying a new carrier when the bolt shears and you are stuck ruining a carrier just to remove the axles. Also, take the driver's axle back for a core when you grab the passenger one. There is satisfaction in sliding the axle in the shortened side the first time and it fitting in perfectly.
I also did a write up on adapting the factory cables to the ford parking brakes. It is in the performance section.