Am doing the head gaskets on a 95 3.0 as we speak. Just got the heads back from the machinist yesterday. Didn't have any Toyota experience but a moderate amount of other mechanical experience. That being said,breaking it down is not that bad, but it is time consuming. The worst part, for me anyway, was taking the time to mark the vacuum lines, didn't want to have any issues putting it back together. Will let you know how it is when I put it back together.
Cost wise, I will probably put in more than the average guy, currently have $300 into the heads(had three burned exhaust valves on drivers side-fairly standard), am going for a more expensive Felpro full engine gasket kit, probably another $200-250, new lead for knock sensor, $25, full timing belt kit/water pump, $150, belts & hoses, $100, starter-$100(only because I never want to change a starter in this vehicle-ever), plus tune-up parts, cap,wires, plugs, pcv, oil, filter, o-rings for injectors, parts cleaner. You get the picture. All in, i'm looking at a grand, I can squeeze that quite a bit, but i'm not. Oh yeah, I'm doing exhaust work as well.
As for the re manufactured engine, if you drop at an engine shop, will cost you up to $2000 to rebuild your motor. Saw a bunch of shops on ebay selling the 3.0 for an average of about $1600-$1700 with core +shipping. Some were higher, some were lower, and the engines were long block, no intakes, up to a complete motor less throttle body. Many options, none cheap, priced then all out.
If I were you, I'd pull the engine and tear it down, see what the block, rings and bearings look like. If good, have the heads redone, reuse whatever parts are good, and do a cheap rebuild. Then drive into the ground. I could have reused a bunch of parts, but decided to go new with all. Good luck to you, as an FYI, I'll be posting about my 3.0 head gasket job in the next week or so, figured someone would be interested.