Hello,
To answer your question in short, there isn't really a way to "speed up" this process, but that shouldn't be the goal in the first place. Keyword research is the foundation upon which you build your rankings, so you should really be prepared to put some serious thought into it.
In terms of making the process more effective, however, there are a few tactics I have used which have helped me. Feel free to follow this checklist:
- Assess your product categories
Presumably you are not dealing with 1000 different products from unique niches. Start by assigning each of these products to a category and using that category as a landing page. Then you can research each category for relevant keywords.
- Assign keywords for each category
I would take no more than 10-20 keywords for each category unless the products you are selling are well-known (and therefore, well-searched). No e-commerce site can rank first for every item they carry.
- Determine the ranking difficulty of your chosen keywords
I use a national keyword checking tool called Authority Metrics (www.authoritymetrics.com) for national keyword research. It shows you organic competition levels and PPC costs along with national monthly searches based on multiple countries. It is not particularly useful for local clients, but as an e-commerce website, I doubt this will impact you. In any case, it will give you more information than Google's Keyword Planner Tool.
- Create your sitemap/category pages
This should be done after you have determined what keywords you can/will be ranking for. My strategy tends to involve a 2-pronged approach where I use 1 sales funnel for low-hanging fruit (long-tail keywords or unique products) and another for large-scale keywords which will take time to rank. This allows you small-scale income very quickly, while also allowing you to build your site organically.
- Create content for each category, and your top-sellers
Obviously you need quality content to rank. I like to focus on a percentage of products that I feel have the best chance of success. There is no hard rule about this, but I typically go for about 5% of my overall product list. Generally speaking, 10% of your products will yield 75% of your overall sales. Find the balancing point between your keyword's monthly searches and the ROI you stand to gain from ranking each of these products.
This has gone beyond keyword research and into sales and CRO, but I hope it helps to give you a helpful outline of my approach to the e-commerce landscape. This process will put you in good shape for establishing your site and getting purchases.
Feel free to follow up with me if you have further questions.
All the best,
Rob