New NSR 250 MC28 rider.

I think I messed up pretty badly. I used 2 stoke oil that is similar to you use on small engines. After just 3-4 miles, I broke down, I was able to ride it back home in 1st gear on and off. I know I need to drain it and some how flush my oil. What else should I be doing? I've been looking for a service manual on the forums but I can only find a parts manual. Any help will be appreciated.

Don't panic yet. Unless you used a 2t oil that isn't suitable for injection systems than you should be ok. Low grade/quality oil will cause the bike to smoke excessively and wear prematurely but not after one ride. You may just have fouled a spark plug so replace those along with replacing your 2t oil. Then start diagnosing from there.

If you didn't seize you're OK. Just clean out the oil tank and oil line to the carbs and replace the spark plugs. There is no oil to flush, what's left in the system will quickly disappear - just don't ride it until you given it time to run through (5 minutes at idel will do). And next time get a good oil - it's one thing you don't want to scrimp on.