Well, I've tidied it up a bit more and added a few net names and .op voltage and current labels, and its obvious that Q1 is hard on, and is dragging the LM317 Adj pin to one LED Vf drop above ground, thus limiting the output to a maximum of 3.28V
The diodes and R3 are dragging the regulator output down. If you increase R3 to 100R, the regulator output goes up to 15.44V before the 555 and charge pump circuit drags it down. However the LM317 model you are using doesn't seem to be very stable and the LMC555 model certainly doesn't like a rapidly varying supply voltage so the simulation time becomes unreasonably long - its a brute and probably indicates its behaviour would be unpredictable in real life.
I assume the 555 and charge pump circuit is meant to be a desulphator - you should get the basic CC/CV charging regulator circuit working first, then redesign the desulphator with a constant supply voltage to the 555, and maybe change to a pumped LC series resonance design powered by the incoming supply to the regulator so that it draws no net DC current from the battery. A choke to isolate the desulphator pulse from the regulator would also be helpful.
Tidied up sim attached with all models and symbols reqquired. Caution: its *S*L*O*W!