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since the CEL was on, do you have a list of the codes present, and what kind of symptoms were you having ?
The leak you are talking about, i assume you meant coolant leaking ? since you used block seal to attempt a repair. I personally am not a fan of using "stop leak" types of additives, as they can cause blocking of areas that you don't want filled. ie: radiator passages, heater cores, things of that nature. now with that said 900 sounds a bit on the high side labor time is listed at 2.6 hours for upper and lower intakes. unless there are some other repairs taking place at the same time i'd get a second opinion.
Have your battery tested, the charging system sounds like its working fine, but that will change if the battery issue isn't addressed. A bad battery can cause the alternator to overwork and burn itself out, so test the battery and replace if neccessary soon.
Not much to go on, so let me ask a few questions. does the shaking only occure as you are accellerating, and change as speed changes, or is the shaking when you brake ? i would recommend having the front steering linkages inspected for warn, or loose parts. i have run into a few chrysler mini-vans with higher mileage with worn motor mounts that shook violently back and forth, another area to look into.
a few things to consider, is it a 3.0l OHV or OHC engine, makes a big difference in cost. also how did the head gaskets "blow" what was the underlying cause for them to fail ie: waterpump, faulty t-stat, plugged radiator. you also need to consider the cost of the repair as opposed to the value of the vehicle. if you have coolant in the oil, and it was run that way for very long, bearing damage has probly occured. in some cases it's more cost effective to replace with a used engine, or a reman'd one. the biggest question when looking at high dollar repairs, How much do you like the vehicle ? and will i get a return for the cost of the repair.
Start with doing a charging system diag, make sure the alternator is putting out enough to charge the battery, if that checks out, then it's time to start looking for a current draw with key off. i assume when you say it won't start, then engine won't crank over ?
i would start by looking for a vacuum leak at the hoses around the intake manifold.
sounds like rotor runout (warped). i would have front end inspected for loose parts and have a brake inspection performed, paying close attention to rotor warpage
that is a way to look for a low contributing cylinder. cold misfires are very common on the 6.0 and when the injector starts to warm up then will begin operating normally. the injector will eventually "puke" and stop completely. there is also a PCM and FICM reprogramming available for cold weather miss fires. i would have a diagnostic run while the engine is cold to determine which cylinder is low. Is there a CEL on ?
had one of these bite me, installed a reman engine with new water pump already installed. the engine would warm up normally and i would get mild heat at idle, once on the road, no heat. the waterpump impeller is plastic and was cracked, just another thing to check.