My vote goes to Warmoth for sure. I have assembled three parts basses with Warmoth bodies and necks now, and I have zero complaints. I am sure that more Warmoth builds will be in my future. IME the quality is great, fit and finish great, etc. Put it together and play, basically. Also, I can echo what micguy says about lead times--what they have quoted to me has always been accurate. Paint takes longer right now, that's just the way it is, but my most recent order was not delayed beyond the lead time they gave me when I issued the order.
If you're looking at Warmoth's Short Scale Bass (SSB) bodies and necks, then options are a bit more limited compared to the 34" scale stuff, like fewer body shapes and 1.5" as the only nut width available, but there is still a lot of customizing you can do. And certain limitations might actually play into your favor (e.g., you don't have to choose between steel rods and paying to upgrade to graphite rods because SSB necks don't require stiffening rods).
I will also add that re: weight and good balance: I've become a pretty big believer in roasted maple necks from Warmoth. My 34" roasted maple neck (w/ graphite rods) is noticeably lighter than the 34" maple neck (w/ steel rods) that I ordered previously. The different stiffening rods certainly are a factor, but I think the roasted maple is also a tad lighter than a regular maple neck as well. If I was building a short/medium scale with a Warmoth SSB body and neck, I'd definitely be going for roasted maple as the neck wood. Just my 2 cents