hmm, never heard of that problem before, but you need the car on ACC i think it is, not really sure what is going on with that, I think you'll have to play around with it unless someone has experience with hat type of issue,
(Edit:, I just re-read your post, and yes you need to key in and the car in ACC, there is an order which you need to do things for it to hook up properly, I think you need the cables connected to the comp. and ssafc, with the computer already turned on and, it helps, with R4 program up, and then turn the car to ACC and then try to connect.. it might be the other way around but if your cursor starts flying around then try it another way.. it helps also if you don't have your mouse plugged in (I have a cordless remote and it makes the cursor fly around if I have it connected when I am trying to connect to the ssafc)
but as far as the tuning, just take away -.1 at a time, for the areas where it is really consistently down in the 10s, you could do -.2 for the first time, (make sure it's only in the areas that are really rich, better safe than sorry), but then just do a few logs/runs after you change the map, and see where it is rich, but I would only do it -.1 at a time, and in the fuel map the x and y axises are the boost and fuel, you just have to scroll over, you can also click on the top left corner of the axises and that will highlight all of the cells in the fuel map, and then just drag one of the axis boxes (so say one of the rpm boxes) to the size that you want, and release, which will make all of the cells that size, and then just do the same for the boost... the only problem, which I don't know what r4 made it like this, is that once you click on the area you want, it will all scrunch up again, so I just click on where I want, and remember how many cells I wanted to change/highlight, and just double check once you change them, that you actually highlighted the correct cells.
It is pretty tedious, but I would seriously read the manual that came with the program that shows you what everything is, I read it a lot of times just to make sure I had a general idea as to what everything was before I even started tuning anything, because if you make a mistake it could turn into a HUGE and very very expensive problem... like say.... your engine blowing