Use the "coin control" features in Electrum: "View -> Show Coins"

Then on the coins tab, simply use "shift+left click" and/or "ctrl+left click" to select say 50-100 inputs at a time... then right click and select "spend". It'll create a transaction setup to spend just those coins, which you can sent to one of your receive addresses. Then "just" repeat that about until you have consolidated all your coins into less than 100 inputs

Once you have it down to under 100 inputs, you should probably be able to spend them all at once.