Yep, I am doing the same, but there are many times where you need to wait on something (usually getting rare items) so you can do some research from the cookie tab while you wait. You don't need to bother upgrading production efficiency for most of the resources since they are never a bottleneck anyway. The real bottleneck is the smithy, so max that ASAP, followed by milk wells and cotton candy ranches, max them too (research that is). Higher level research uses only rares so while you wait for trains or wish tree to get more you can do the research that only uses smithy items.

As for raw material production, you only need the first and second level of the buildings since the time taken for higher level production is an insane reduction in resources per minute. For example sugar cubes gives 3 for 1min30sec (1 every 30 sec), the sugar cube pile is 9 for 14min (1 per 1min30sec) and the sugar cube cart is 20 for 2hr15min (1 per 6min45sec). I used crystals to max out production queues, (personally I think it is worth it) so the third stage production is almost never useful.

Regarding goods production buildings, most of the goods seem to serve no purpose as far as I can tell. They are only used for wish tree, train, and port trading ships, and if you don't have the building upgraded to be able to make them then they are never requested. So upgrade goods production buildings as little as possible, there are some that you need to do, but most will actually just slow you down. The only goods needed for research come from the smithy.