John -

If your machine shop didn't do a good job, then yes - the threaded depth will be different for each bolt. If your engine is like mine, you'll also find a difference from one side of the block to the other and from the end holes to the middle ones.

Clean the head bolt threads on a wire wheel brush, then with solvent and let them dry. Run each bolt into the deck hole you assign it and stop just as you feel it start to drag. With a dial caliper, measure the distance from the deck to the underside of the bolt head and write down the measurement. Measure the thickness of the washer with the calipers. Measure the thickness of the head at that bolt location. Deduct the head thickness and washer thickness from the bolt measurement. You should have a negative number for a result. If not, your machine shop didn't do the job you asked them to do and I would recommend not assembling the heads until all bolts have sufficient clamping range.

Once you're satisfied that the bolt is ok at that hole location, don't mix it up with another location. Lay the bolts out with their dedicated washer in an order that you can later determine which one goes where.

Install the head gasket dry - no sealer should be used. Make certain the gasket is clean - as with the heads and deck.

I'm having trouble accessing my email, so I'll describe the tightening sequence as best I can - if someone else can email the picture from the FSM, it might be easier to understand:

Driver Side

As you face the head with the front of the engine to your left, there are 8 bolts, 4 on the top row and 4 on the bottom row. Draw a sketch of the following number pattern and you'll see that tightening begins in the middle of the head and runs in a clockwise circle. On your sketch, number the top row of bolts left-to-right: 8/4/1/5 and number the bottom row left-to-right: 7/3/2/6. Tighten in series - #1/2/3/4/5/6/7/8 in stages until all are at 80 lb-ft and go around again at 80 lb-ft to double check.

Passenger Side

As you face the head with the front of the engine to your right, number the top row left-to-right: 8/4/1/5 and the lower row: 7/3/2/6. Again, begin with #1 and follow the numerical sequence.

I know the procedure I'm recommending sounds picky, but I think it's absolutely critical in a 3.0L engine to ensure a good build.

Frank