1) How many days? I think it depends on how you're attacking this trip. If you only want to see the stuff that's different from WDW or isn't in WDW at all, I think one day per park would be good. Or if you wouldn't ride the "kiddie" rides like the Fantasyland dark rides. If you're approaching this like another trip to WDW (if that makes any sense) and you want to hit all of the headliners and most of the attractions in both parks, then I'd say go with a three or four day park hopper minimum. Personally, I look at a trip to DLR like I do a trip to WDW-- when I go to WDW, I usually go for 7-10 days and go to MK and Epcot 3 days, DAK and DHS 2 days or something like that and do my favorites a bunch of times... I don't just check attractions off a list and say, "Rode Space Mountain once... done with that!" I ride all my favorites a bunch and visit the parks multiple times! Why should DLR be any different? DLR has about the same number of attractions as WDW, so you definitely won't be bored if that's what you're worried about.
2) Differences? A few.
I love this screen grab I took, although it is a little hard to know exactly what you're looking at without ever having been to Disneyland. The important thing to take away is that there is a roughly equal number of attractions as is in all of WDW crammed into a space roughly the size of Epcot:
(Same zoom level)
I also find the variety and quality in the counter service food to be much better at Disneyland. I think it's because Disney knows how easy it is for people to run across the street or stop on the way home for food. Very different than WDW, where you are usually miles from off-site restaurants. Also, table service dining is not as big a thing at DLR. There are not quite as many TS restaurants and you certainly don't need ADR's 180 days out.
3) Use
Wikimapia. Almost without exception, all of those hotels on Harbor Blvd (the street just east of DLR) are pretty cheap, pretty well-reviewed and are closer to both parks than the Contemporary is to MK. It's definitely worth playing around with because each hotel has different amenities, different discounts, different quality breakfasts or no breakfast, some charge for parking. One hotel didn't charge for parking, but gave something like a 20% discount if you didn't bring a car!
4) The crowds for the first two weeks of June next year are mid-level. There is a very different crowd pattern than WDW, though, because of the amount of locals. Monday-Thursday is very different from Friday-Sunday. Also, the crowds grow later in the day when people drop by after work. Remember that they do not enforce the end of the Fastpass window yet at DLR, so you could get Fastpasses during the day when the crowds are somewhat less and use them at night when more locals drop in. As a side effect of the crowd pattern, they don't necessarily run fireworks or Fantasmic every night. Your trip might fall into "summer" time, though, where I believe they run every night. I have heard sort of anecdotally that the lines don't get crazy because the locals don't have the urgency to ride the rides like tourists do. Line for Splash is 80 minutes? Eh, I'll just ride it next week.
5)Must do's:
-Indy
-Space Mountain: completely different coaster than WDW's. Very smooth, and with onboard audio by Michael Giacchino. The audio is in the cars, so it is synched to the ride. The MK's is not onboard, so it is more like general atmosphere music. Also has effects that the MK doesn't.
-All of Carsland
-Soarin' : just because it's usually like a 20-30 minute wait and I bet you've never seen it like that at Epcot!
