I would find a smaller HONEST mechanic that is recommended by other Honda owners/DIYers. I know which guys I can take my car to when I can't handle a repair job, so someone in your area should know also.
If you find that mechanic, then discuss all that you want done and see if he/she will work with you. He/she will also where to find a GOOD used tranny becuase they don't want to do all that work again either.
Then tell them you want to reseal the motor (oil pan, valve cover, rear main, cam seals, crank seal), replace the headgasket (headwork shouldn't be needed, but that's up to you-I would have the seals replaced, but that's it), the timing belt, tensioner and water pump, thermostat, plugs, all the drive belts, tranny swapped in and tie rods replaced. The shop will do an alignment so make sure you go in with new tires when you have the work done.
It will cost a lot, but if you do all of this stuff seperately, the repeated labor would kill ya.

I will be doing this soon to a 96 Accord that someone didn't want to spend the cash on (I got it for $500), now they have to go pay for a NEW car.

Post the toal guesstimate that the shop you choose charges, just curious.