I got a 400F engine rebuilt by a very reputable shop known for good work on old SOHC 4s for around $700 labor. I had two engines that I dropped off, one extra that I bought for $150 in case they needed spares, and another that I had torn down and painted. Didn't need any extra work like machining, and the oem parts I needed were probably around $300 or less in total.
This was in Phoenix in 2011 or so, and the shop is no longer around.
$3-5K seems pretty excessive to me, but I guess it depends on where you are and what a shop thinks you can pay, as well as what work the engine needs. But thinking about hourly rate vs how many hours it would take to do the job (and of course depending on what needs to get done) I think you could get it done for less, unless the shop is charging $200 an hour. The shop rate I paid was $60 or $70 an hour, IIRC.