My bike is a 2006 Electra X. I've had this plate off, and was impressed by the closeness of fit. This was two years ago and I have to look at the parts catalog to refresh my memory. Like everything else on this bike, after you've done it once you will never again need the manual.
The illustration shows one nyloc nut on the mainshaft: #550025.
There are the four nuts you have taken off, #550043.
There are also two dowels (#550094/a) that locate the plate on the side of the transmission box; the illustration shows them on the bottom right and top left, and it looks like they are under the washers for two of the holding nuts. I remember that these two are the cause of the problem you are having, simply because the tolerances are so close that the plate does not want to rock with them in there. This is good and why the dowels are there: you don't want the plate to rock when the transmission is doing its thing.
These two dowels, plus the fact that with the thick transmission fluid all over everything the air can't get between the mating surfaces, is why the plate does not want to come off. I tried the kickstart lever trick and don't recommend it. I recommend using your fingers on the outer edges of the plate like a pull tool, tugging and rocking, then moving to a different location and tugging again. Put your hands 180 degrees apart, and rock, too. Be careful - on my bike the inside edges are very sharp. Not burred - sharp. I ended up using clean work gloves. Don't pry with anything, and it might be wise to have a helper stand on the other side of the bike and hold it upright, or tie the bike firmly in place.
The tolerances for the two dowels are so close that you will have trouble getting them back in, even though you are sitting there looking right at the assembly.
Whenever I get the chance I recommend getting the spare parts catalogue (sic.) The dealer gave me a copy with the bike, and it is worth its weight in all the manuals in the world. The illustrations are so good that if you had to you could get by just with it.
Anyway, this is what I remember. Work slowly and watch what you are doing, and above all DO NOT pry with anything. Good luck.
Paul