Start eliminating some of the aftermarket parts. If your throttle body is a BBK, they are notorious for causing issues. Put the stock TB back on and see if that helps. Also the stock 60mm throttle body is more than enough for a stock headed motor so you actually will see no gain going to the 70mm. I'd also pull the MSD box since you don't need it and its another potential cause for having an issue.
Finally, you did the cap and rotor but those rarely, if ever go bad on a 5.0. The distributor itself, however, is a known problem on these cars. Pull the cap off the dizzy and look in there, if you see a silvery powder in there the PIP (pickup) is likely the culprit. If you have a shop press you can replace just the PIP, if not you can get a rebuilt distributor for around $100.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.