$5k isn't too far fetched for a short block, open a catalog and order all new parts, drop them off at a decent shop and then go pick it up, it sounds about right.
I've always done my own engine assembly and never had any issues, its all about checking and rechecking and using good parts.
For the stroker I'm setting up:
Eagle rods:$500
Eagle Forged crank: $800
Arias pistons: $700
I'm at $2100 and haven't even had the machine work done yet. Don't forget gaskets, bearings and bolts.
I'll have about $3500 in my short block before its finished. On top of that will be a set of heads, another $2k and then I've still got to factor in a power adder and fuel system and the broken transmission that will come from the added power along w/ axles.
Then I'll have to sit back and hope that it actually runs well enough to drive to work everyday.