Lot of wise words been said already...
My take, for what it's worth is: don't expect to make a profit, but do expect a bass that is significantly better than you could afford otherwise and just right for YOU. The reason its value is less for others is that they may be looking for something different and they will always fear 'home bodged' rather than professionally upgraded.
The upgraded Squier Jaguar Bass I've recently posted on Gear Porn is absolutely done for my own use. It's absolutely not to everyone's taste but I don't give a t**s, because I didn't do it for them To me, it looks fabulous, it plays just right, it sounds so much better than the original and has given me a bucketload of satisfaction. For £180 s/h, £40 of veneer, sandpaper and varnish and £25 for strings, I have a guitar worth £900 in my eyes, but to anyone else, I have a £299 Squier VM Jaquar Bass that looks a bit fancy. I did do a similar thing to an Ibanez entry-level bass and I DID make a profit, but only by selling it to a nepalese buddhist who plays in a heay metal band...and how many of those come along at just the right time
Having set my realistic expectations, my take on the order is: first make sure you're starting with a 'decent bit of wood' with a neck that's playable - all of the major names that sell good quality expensive guitars cannot risk denting their reputation with rubbish entry levels so we're talking here Yamaha; Squier; Ibanez etc, etc. Then it's: strings; setup (especially pickup heights and balance); pickups; bridge; tuners.
...and it really is great, great fun!
Andy