Well as far as the lower control arm being stuck to the knuckle, you will have to take the lower arm off with the knuckle, and then put it in a big vise and then you should be able to hit the bolt out and get new one's, and if the lower control arm ball joint is toast by this point, the ribbets will need to be gridded off, and you will need to go to Autozone for a replacement set that come with new bolts.
Now as far as the sub-frame bolts being stuck, you just need to apply enough pressure, a good flexbar or otherwise known as breaker bar will do the trick, if you break em, they can be replaced, either from the junkyard from one's that you can get off, or new one's from Ford.
I just got done doing a flywheel and clutch kit in my 03 2.3l. I'm currently almost all back together.
Let me know if problems persist. Here are some pics of what I had to do.
Watch it on getting them out the knuckle too, might need one of these.
And to get the half shaft out, cause it has a clip on the end, you will need one of these to hammer it out.
Hope this helps.