1.  That sounds like the choke is not working properly.  Check to make sure the linkages are clean and work freely.
2.   I guess it depends on what you want.  Do you only want them to blink with the turn signals, or do you still want them to function as side marker lights, and blink as well?  Maybe you could accomplish this by running the side marker ground wire to the turn signal wire.
Just a thought, I haven't done this myself.
3-5.  Don't know
6.  No doubt, but so is everybody else who still drives Pintos!  

If you want it drivable, your priorities should be 1, 5, 2, and then 3 and 4 in whichever order you wish.

Now, for your questions:

1) Don't know without looking at it.

2) No, not difficult at all. As Straw Boss says, you're simply rerouting the wires from the side lights to splice into the wiring for the front/rear turn signals.

3a) and 3b) Read through some posts on this site. Also, look at the May 2004 Hot Rod, pp. 105-107. There's a description of swapping an '84 Mustang to 5-lug patterns with larger disk brakes on all 4 corners. While the part numbers may not be accurate for your application, reading about what's involved may help you make decisions...es pecially since you mention your lack of mechanical knowledge and tools.

4) I own a wagon and don't know the specs on runabouts and hatchbacks. What I do know is that if you go to a salvage yard they can tell you if the swap works. They have computer programs that let them what parts are interchangeabl e. Also, if you develop a good reporte with knowledgeable clerks at your local auto parts store, they can often tell you if a swap works. Remember, both places make their money by selling you the replacement parts. It's in their best interest to give you the info so that they can make a sale and keep you as a happy, repeat customer. You just have to go about it in a "you-scratch-my-back-and-I'll-scratch-yours" manner because a lot of times they'll just say "I don't know" if they don't see any profit in giving you the answer. I've found that by becoming a regular customer at the parts store I'm more apt to get a straight answer from the clerk. Yeah, I pay a few pennies more for a quart of oil over the big box discount stores, but it's worth it. If you mention the word "Pinto" to the average Wal-Mart auto "specialist," you'll get a blank stare followed by "Aren't those the cars that blow up?" It also helps that I dropped $225 on an engine hoist from the parts store. Now, the moment I walk in the door, I have a clerk right there asking how they can help me. And they're more than happy to discuss my car needs with me...even if all I'm walking out the door with is a couple quarts of oil. This is also a great way to get help with your brake swap info.

5) Are you going to redo the vinyl or go with the "hard" look? It'll look ugly under the vinyl when you rip it off. Most cars I've seen with the half-vinyl removed have a distinct difference in paint quality. Plus, you wind up with the edge trim just sitting there. If it's been loose for a while, you may discover some heavy-duty rust spots from pooling water that have been conceiled by the vinyl and the head-liner.

6) Yes, no, and half the time you will be driven there.