I'm sorry to say that there is no way to get this info using the MWS API. The MWS API doesn't have any relative information, that is, it doesn't know anything about other sellers' items so there is no way to see what your items are priced at relative to others (which is the info you would need to determine if you own the Buy Box).
As you already know, you can get this info through the Product Advertising API but with the new limitations in place this may not be practical for the size of your inventory (would take three days two and a half hours at 20,000 items per day hour). The "re-pricing" service that you've used in the past was most likely affected by the new limitations. However, any existing accounts were given a grace period to change their software. The new limitations will go into effect for these accounts on February 12, 2012.
The only other option open to you is to get the info from the site (screen scrape). This isn't a very attractive alternative due to the latency issues but if you've got the infrastructure to do massive amounts of parallel calls then go for it. In certain situations I prefer to get this type of info from the site since this is what the buyers are seeing (most current info). In the past I've seen data coming from the Product Advertising API that was out of date or just plain wrong.
The limits are defined in the documentation under the obscure subtitle of "Efficiency Guidelines" and is located here (at the bottom of the page).
I must admit that it's been a while since I had worked with the PA-API and had forgotten the limits. I thought it was something like 2,000 a day but it's actually 2,000 per hour at one call per second. If you're making calls too quickly they'll return a 503 response which is documented here.
Update: Amazon has added a Products API to the MWS APIs. The GetCompetitivePricingForSKU gives you pricing information similar to the Product Advertising API's ItemLookup function. With this information you should be able to determine the price of the Buy Box owner.
