Looking at your trailer photo it appear the bunk supports start at the rear main frame and then run inboard to a point of more than 18 inches from the main part of the frame or the rear end of the bunks is about 6 feet wide and the front of the bunks is 4 feet or less.
This allows the narrower stern to sink down in-between the bunks at the rear. Your photo of boat and trailer looks like the waterline of the hull is not level with the mainframe of the trailer, high in the front and low in the back?
I also see the construction of the trailer at the rear has NO cross members higher than the axle right in the center of the boat allowing for an unobstructed opening for the submerged keel to enter the trailer. This looks great but is it needed to be constructed this way? Think of your launch ramp, it’s not level, the water is. The back end of your trailer submerged at the launch ramp is 2 feet or more below the bottom of the keel. The mid section of the hull and stern is still floating above the bunks even when the bow is the whole way forward on the trailer. That's why it’s hard to get the stern to line up at the back of the trailer. Do you notice that the hull is up tight against the trailer bow chock in the water but is pulled away when the boat and trailer is hauled out of the water?
Here’s what I would do from what I can see from your photos and if the above statements seams to describe everything somewhat;
Remove the keel roller and add a cross member behind the axle to support a 2 x 8 keel bunk, extending up to the main cross member where the front of your present bunks are attached. I would make this keel bunk level with the outside mainframe and no lower than the bottom of this mainframe. Being no lower than the mainframe would allow the same clearance as the axle has to the mainframe and also allows the hull to be as low as possible on the trailer. Your present keel roller looks like it may be 4 inches lower than the bottom of the mainframes and very close to the axle height as you have stated. Stretch a string across the bottom of the trailer at the location of the keel roller to see how low it is, what ever this distance is plus the thickness of a 2x8 is the height you need to raise each hull bunk.
Now the small bow roller, great aid when retrieving the boat. Present location is too far forward should be less than 1/2 the distance from the end of bunks and about 1/2 to 3/4 inch below the hull when hull is in it’s final resting position. This clearance allows for the flexing of the trailer on rough roads, as stated this roller is only an aid in loading the boat, not support the hull! Think of this, the boat is floating level on the water the trailer’s at an angle on the launch ramp, as you pull the hull forward the hull has to ride up over the front of the bunks. Roller is further up the ramp than the ends of the bunks so it is not as deep in the water, the front bottom of the bow now hits this roller before the ends of the bunks and helps lift the front of the hull up out of the water and help clear the front edge of the bunks. At the same time the bow is lifting the stern is sinking to start mirroring the angle of the trailer on the ramp.
The bow winch must be level or slightly higher than the bow eye, this helps to continue lifting the bow to match the trailer angle, if it is lower, then your pulling the bow down and lifting the stern so when the boat is hauled from the water the stern settles down on the back of the bunks and the bow lifts up and away from the bow chock.
Keel guides are a must but they will only work if they are high enough, remember the hull and keel is floating above the trailer because of the angled launch ramp so guides must be almost as high as the hull bunks to come in contact with the keel as it’s floating above the trailer.
I’ve provided illustrations of the mods I would perform on your trailer.
I’ve been working on a launch ramp illustration showing what is possibly going on with the hull and trailer and also the keel. The bow roller really works great if it is placed properly.
I included a photo of my bow roller and the gap between it and the trailer, been using this bow roller for about 12 years.