Does the other system specifically say that there is NO limit at all to the number of questions? Often they just say that from the system itself there is no limit. Later they often tell you: well, unfortunately the database doesn't support that many questions. I am not saying that this is the case, but it is good to ask this specifically.
I think 3000 questions will not be possible in Limesurvey, if you can't split your survey in 2 or 3 and join them via the endurl, especially if you have multiple choice questions. From what I know, the number of columns depends on the database engine.
Have a look here, this should explain things pretty well:
www.limesurvey.org/manual/General_FAQ#Ha...oftware_requirements
If you can't split the survey in 2 or 3, your maximum number will be somewhere around 1000 questions or even less (depending on whether you use a lot of multiple choice questions or matrix questions, which need one column per answer option!).
Maybe your solution would be to use PostgreSQL (see the link to the manual), which allows up to 1600 and there are options to increase that number. But I have no experience with that.