Yes and no. There's a difference between the 88, 89, and 90-91. The comparison file is a PDF posted somewhere here on the site- search for it.
Basically, there are two disc/pressure plate sizes, and there are two input shaft sizes on the transmission. You can build a hybrid setup- just make sure that you have the right pressure plate to bolt up to your flywheel, and that you have the right disc to fit on the input shaft for your chosen transmission.
Years DO matter.
As far as DX vs LX, the difference is in the chassis type. All USDM sedans had 4.058 final drives. The non-HF/Si 5 speeds have 3.888 final drives. The Si has a 4.250 final drive. The 1-5 ratios between the DX, LX, EX and Si are all the same.
For the best gas mileage in a 5 speed, the HF transmission would be best- but your performance will suck. The best mileage transmission where your performance WON'T suck too hard would be the hatchback DX transmission. It's also going to be the most common in the junkyards.