We've had Cruiser a week tomorrow. He's eating good now and playing a lot. He's much better. He's doing good with the potty training for the most part. He sleeps good at night. Now on to things we haven't started:
How often should I give him a bath? He had one last Thursday at the breeder's. I have brushed in almost everyday but I have given him a bath.
I give Meeko a bath once a week and his skin is fine. If you find that your baby's skin is getting dry you can wait 2 weeks for every bath. I bathe him with a soap less shampoo. It's better, especially for puppies, because they usually wiggle around and you don't want to get soap in their eyes. The shampoo i use is made with Oatmeal and Aloe. It's better for their skin, and prevents drying. I got mine from my vet. It smells great too!
How often do his ears need to be cleaned?
Like the previous poster mentioned you should be plucking the hair in his ears. It's really simple. Petsmart sells a powder that numbs their ear and then you just use tweezers to pluck the hairs in their ear canal. As far as cleaning their ears, I got an ear solution from my vet that has alcohol in it and has a fruity smell (the ones I found at Petsmart had a horrible smell) After each bathroom I put a few drops in his ear and rub the base of his ear and let him shake. You do this after the bath, because if you get any water in the ear by accident, the alcohol in the solution will help dry it up. Getting water in the ear causes ear infections, so you should be very careful. I've read that come people put cotton on the ears when they bathe their babies.
When should I start brushing his teeth? Do you do it everyday?
Like the previous users said start early and do it every day. There's also a product called Petzlife that is really great. If you google their website, somewhere on the website they'll give you a list of shops that carry it. I use the gel form. Just take a Q-tip and rub a little bit around the teeth and it works great getting the plaque off. I use the Petzlife 3 times a week and then brush his teeth the other days. It's also easier if you go buy a toddlers toothbrush. They are the perfect size for their mouths 
When can he start walking on a leash? We haven't attempted to put the harness on him yet.
The earlier the better! 
I just left the harness on for an hour or two when I was home watching him. It took a while for him to get use to it. Once it didn't bother him, I started with the harness. I'd just attach it to his harness and let him drag it around for a while. When he stopped playing with the leash, I started picking it up and following him around holding it. After a few days he was fine. If he's slow with the leash, grab a few pieces of food and walk ahead of him dropping a line of kibble. He should follow you eating the kibble.
What age is a good age to take him to puppy kindergarten? Is Petsmart or Petco okay for this?
I used Petsmart and loved it. It's all about your instructor tho. If you can go and check out the instructors there. Watch a few classes and see who you like best. Petsmart won't let you start untill you've had your puppy shots. I started with Meeko when he was about 3 months.
With all the problems with had with the vaccines and the emergency vet, etc., I am thinking of switching vets already. Is Banfield (attached to Petsmart) okay? They have a good plan cost wise.
I can't answer this, because I didn't use them. sorry.
I am leary about giving him the heartworm tablet that the vet gave us because the reaction he had to the vaccines. Also, he has to go on a medicine because his stool sample came back positive for giardi (spelling?). She said it's a powder to mix with the food and we should start it next week. Should I wait to give him the heartworm tablet the following week? The breeder suggested only giving him half the tablet. What do you think?
What brand did your vet give you? I don't know the problems you've had with your baby but, I wouldn't split it. How big is he? I'd wait for some other members to give their opinions of this. Definitely get the giardi fixed tho. Thats a nasty little parasite.
How harmful would bird seed be to him? I posted before that we have pet cockatiels. They are messy and there's always a little seed on the floor. Well, being the little cruiser he is, he is always cruising around and trying to eat the seed. I stop him, of course, but I'm sure he's already eaten a couple of seeds. We will do a better job of sweeping and vacuuming, but we're never going to get it all. Hopefully it's not too terrible for him if he ingests a few seeds.
I don't have birds but, I'm sure they aren't good for him. I'd try my best to keep him from getting to the seeds. I don't know what you could do but, it's better to be safe than sorry. it's not worth the chance of your baby eating of lot of seeds and getting sick.
What do you do about cords? He keeps trying to chew the cords to the lamps in the living room. There is no light fixture in the ceiling so we have to have the lamps. I keep distracting him from them but he gravitates back there.
Meeko gave him hard time with cords for the 1st week. I nipped that in the bud tho. Every time he goes for them just tell him firmly no and hand him a toy. This applies for him trying to bit your hands too! It's better to stop that before it turns into a problem. Just keep offering him toys he can chew on. Try bitter apple, you can get it from Petsmart. Bitter apple didn't work for Meeko tho, he loved it! 
I had to rub tabasco sauce on things for him. He loved metal! So I had to put tabasco sauce on the clip of his leash.
I guess that's enough for now! I really appreciate everyone's helpful comments.