I'm going to guess a lot of this is the guitar and not the electronics. The tough part is then finding something you like, not doing the actual work - in which case it's hard to suggest taking it to a shop, since they'll do what you tell them to, and you could just end up back in the same boat, repeatedly.
You're sort of at a crossroads- keep playing with it until you find something you like, or just sell it and look for something else. If you want to play with it, then you're best to do the wiring yourself (assuming you're comfortable with that- and we can certainly help you out).
The question is, what's the guitar missing? Then you can try to find something that best suits it. If you don't like the characteristics of the pickups, is it missing highs or mids? Something is missing to your ears.
Re pickups- personally I like the Transition in the bridge with 500k pots. I have one in an LIII and my Morse. But the stock Axis humbucker is great- the Dimarzio AT-1 is pretty close if you want to go that route.
Singles are tougher- there are so many. Noiseless are great, but always missing something on clean sounds. Not sure what the stock ones were. I quite like the singles in the Albert Lee, and they're Duncan APS-2 (readily available and not expensive), so that's an option to consider.
What saddles are on the guitar- vintage or block? I've always preferred the vintage ones, you get a little more 'zing' out of the guitar.