From a hobbyist perspective:
I just picked up a toaster oven with a convection bake mode, no mods at all. The convection bake mode is important, as it more evenly distributes the temperature in the oven which prevents hot spots from frying components or cold spots from forming cold solder joints. I have used older toaster ovens, and they work just fine for hobbyist work, but if you're going to pick up a new one then spend the extra $10 or so to get convection.
I have successfully reflowed many boards with different ICs and have never had an issue. I can't remember the specifics, but I usually give it roughly 90 seconds to come to a "warm-up" temperature, then jack it up to my final baking temperature (I think it spends about a minute or two in that phase). Check your datasheets to make sure your components can handle whatever temperature your solder paste melts at, and for how long. I pretty much eyeball it when I first do a board of a given type to see when different parts reflow based on the amount of solder paste I use, but it's all been pretty similar in my smallish projects.
As far as templates/stencils go, I don't bother unless I have lots of fine-pitched ICs. Get yourself a solder paste kit with a syringe and different tips, and play with those (I used this one from Celeritous: http://www.celeritous.com/estore/index.php?main_page=product_info&products_id=47 there's also a lead-free version). All you need is a sufficient blob of solder paste, surface tension really does 90% of the work if you don't put too much on. I figured out "how much" through trial and error on a few spare boards.
I think if you're not trying to sell stuff and you're not working with sensitive components, no mods are required. In my experience, components are pretty darn robust all things considered, and nothing beats the learning process of watching solder paste reflow on some old boards (and SMT components, if you have some to spare). You'll know when you really need to address the issues you brought up.
Honestly, I wouldn't try to solder my own BGA's. I know this doesn't directly address your issues, but hear me out.
It takes a lot of work and effort to solder a BGA. There's a lot of trial and error. A lot of messed up test boards. But then it's soldered. Now what?
Now you have to prove that it's soldered correctly. For that you need one or more of the following: JTAG test (US$10k, never has 100% coverage), optical inspection (US$20k for the equipment), or X-Rays (US$500k). The cost of doing these tests is too much for the normal hobbyist, and is even beyond many small companies.
Skipping those tests, you proceed with debugging your PCB. And let's say that the BGA is a complex CPU. Inevitably you'll find a bug. The CPU will randomly crash. Is it your software, your electrical design, or the soldering on the BGA that's causing the problem? Debugging this, in light of some possibly problematic soldering, is going to be terrible. It will add a lot of time to your debug process, possibly months, and you'll loose a lot of hair on your head. And then you can repeat this for the next major bug.
Without confidence that your soldering is perfect, you will always have this dark cloud over your head. Every little bug that shows up "could be a BGA soldering problem". This is made worse if you have multiple engineers working on the same PCB since the software guy will be questioning the hardware guy, etc.
Then, even if the BGA soldering is perfect, did the chip get too hot? Did you destroy the chip by getting it too hot? Even on modern assembly lines this is an issue. But with the proper equipment you can adjust and measure the temperature profiles to at least get you in the right ballpark. On one board I did recently, the BGA's were being damaged. The solder balls looked great, but under a very nice X-Ray machine we could see that the gold bond wires melted from the heat.
I've been there. Not at the hobbiest level, but professionally as we were bringing up new boards while the assembly shop was learning to do BGA's. We had no JTag. No optical inspection. And the X-Rays were terrible. Our PCB had 11 BGA's on them. That was 2 years of hell I don't wish to repeat.
So, here's my recommendation:
Get someone who has the proper equipment, training, and experience to solder your BGA's. There are a lot of contract manufacturers that'll do a single BGA. It takes money, but that's way less than the time you'll spend trying to debug your own soldering.
If you must do it yourself, then you should get the proper equipment, training, and figure out how to get the experience required. For this to pay off in the end, you need to have a large enough company and need to justify the huge amount of time and money that you'll put into this.
But I would never try to just kludge something together. That's a recipe for, um, bad stuff.
Best Answer
Depends on who's paying the guy who's doing it, what he'd be doing if he weren't hand-assembling, and what the boards look like. As a number for comparison, my US domestic assembly experiences seem to come in at around 6.5 cents per pad (maybe a bit more at low volume), plus NRE's.
Also depends on what your goals are for the assembly. Do you need it done, or do you need it done inexpensively? At less than 100/year, I'd assume the price of the PCB has not much to do with your business model, but I could be wrong. If this is the case, I think the assembly method you describe, when carried out by an experienced assembler, and followed by good QC testing, is an OK approach.