That's a cool looking bass, and you've gone down a very similar route to me. I had a VM Precision and upgraded it with a Gotoh 201 initially, and then a 203 for a more 'vintage' look. I also had a 'Thumper', CTS pots, Switchcraft jack, Orange Drop cap, cloth-covered wiring, full 3M copper shielding to all cavities and back of pickguard and a set of silky-smooth Grover 142 tuners. It was a lovely bass and sounded great but I wanted to try something else so built a Mk II. This has a Squier VM Jaguar neck on a Westfield P-copy body and is fitted with a Bare Knuckle '58 pattern pickup and a Tusq nut. Otherwise all the hardware and electrics were transplanted from the Mk I. The body and neck were stripped down and refinished in genuine nitrocellulose lacquer, and I fitted Fender reissue bridge and pickup covers and a 'tug bar' for a totally vintage vibe. I modelled it on a Fender Custom Shop '62 reissue (photo 1) and it represents five years of teaching myself guitar building on possibly a dozen different instruments. It plays as good as any bass I've ever tried (including Custom Shops) and for a total cost of about £400!
With regard to your too-high nut (they all have them) my solution was to gently tap the nut out sideways and then run the bottom face across some #400 wet & dry, being careful to keep it level and apply even pressure. I just did a bit at a time and checked progress by slipping the nut back into the slot and retuning until it was just right. A couple of drops of superglue to finish and the playability was transformed, more so than by fret-levelling or any other mod I've made. It's an easy DIY job and if you fit a new nut and f*** it up you can always try again with another one or revert to the original... they're cheap as chips. You may find my FB page useful: https://www.facebook.com/howtoruinaperfectlygoodguitar/