When you mention a "new crate engine" do you mean brand new never used or do you mean "new" as in overhauled a used engine to as new specs?. Yes you should purchase the following product brand new:
--Vacuum hoses, engine & transmission mounts, EGR valve, PCV valve,
--Oxygen Sensor,etc. (You don't have to buy them if the parts are in good condition; however, I really do recommend you replace them, it's just cheap insurance. You don't want to have any problems after installing a new or rebuilt engine!). As far as haggling with engine shops go, that's a tough one to call, some shops will have fixed prices yet others will SOMETIMES reduce the price, even if it's very minimal. Some things you could do to reduce the cost, since your dad works in a shop....is you guys could pull the engine out and take it to the machine shop then after it's overhauled put it back in and add all the new hoses, emissions equipment and mounts....that alone will save you some money because rebuild shops charge you to remove & reinstall the engine. Or you could ask your dad to recommend a shop to you since your dad has contacts, they could reduce the amount you pay!!. Insted of the overhaul, you could remove the old engine install the new one and replace the required components with your dad's help. Top heavy, I know what you mean my S10 Blazer feels that way it's only got 30" tires but it takes me to some pretty awesome places!!. Good luck on your home shopping, the garage is the most important thing (at least for me)!!. The winter time will probably be the best time for the install, since you will most likely have the time to do all the work. Take it easy!!