i don't know of any shop that will rebuild a motor while it is in the car.
i plan on rebuilding my 302 just for the experience after the 410 is put in. if you shop around on corral, you can sometimes find good deals on 331 and 347 kits. i just got a CHP 331 kit from a guy on corral (without crank and rings) for $300 shipped. and the pistons are already pressed on. add a 331 crank and new rings and bearings, and i'm looking at about $600 ready to go.
i have no idea what i'll do with it when i am done, because i will already have my engine in my car. so i'll probably get it dynoed and end up selling it at cost over on corral. but that is probably 3-6 months away. i already have some ported windsor senior heads and a typhoon intake for it.
or coasthigh.com has a sale on 347 kits now, $799 iirc.
http://www.coasthigh.com/Specials/Specials_current.htm
from reading about it, it looks like the most time consuming part is fitting the rings.
if you are going rebuild the bottom end, you should do it right. that is the hardest part to fix later.
i would get the block bored .030 over in addition to the honing while it was out; then, you know the cylinders are all perfectly round. don't go over .030 over or the block's strength is compromised. you should also have the main journals checked because they might need honing. it would suck to rebuild it and have problems because the main bearings were out of round.
i'd have the machine shop install the cam bearings. they should charge less than the price of the tool.
people usually have the block decked too while it is out, to make sure the cylinder head surfaces are perfectly flat.
other machine shop costs you might not be aware of are balancing the rotating assembly and align honing if you plan to use a girdle. lastly, most shops recommend honing with a torque plate because that way the cylinders are the way they would be with heads on them during the honing, which makes for better honing and therefore better ring sealing. honing with a torque plate usually costs more than without the torque plate.
finally, when i was going 331 originally, i found this. m&r engines seems very respectable and the price on their economy 331 is very good. they must get great discounts on their kits.
http://cgi.ebay.com/ebaymotors/FORD...005QQitemZ150064617502QQrdZ1QQsspagenameZWDVW