One thing to keep in mind on your '90 is the fuel pump, electric or block mounted? If you have a block mounted pump make sure any new block you get has the hole drilled for it. Some of the newer GM blocks do not.
That's more reasonable than I thought for short block. You can also get a brand new 350 shortblock from GM for around $2000 and put your heads, cam and tin work on it. As mentioined, advantage to building one is you can have the bottom end balanced, you can square deck and align hone the block, and upgrade heads if you want. On the other hand the Vortec 350 is pretty solid in stock form anyway and will run a long time if taken care of. I wouldn't go crazy upgrading parts unless you plan on making some major changes later on, the stock parts are pretty solid as is. When I did mine I was switching from 5.0 to 5.7 so I needed the bottom end anyway. Unless your previous engine suffered some damage I wouldn't be afraid of using your crank if they check out, and even the rods if you get them reworked and put new bolts in. One thing I would suggest since the newer blocks will already be set up for it, would be to look into getting a stock roller cam setup. Its worth it in my opinion for the extra power especially with Vortecs. The stock marine cam is pretty easy to come by too, its not big but runs out pretty good.
One thing I wish I had considered more is making it a 383 while I was at it. Wouldn't have cost anymore at the time but I was concerned about the drive since we do a lot of skiing and hard takeoffs. It probably would have been fine though looking back. We dyno'd it to break it in and even with stock cam it still made 350HP, nice increase over a sickly 305 at the time.