Assaf,

>>1) Can we upgrade to the source code license (pay only the difference between the two licenses)? 

Yes, all you need to pay is the price difference.

>>2) We wish to pay not through paypal. - how could this be done for this kind of upgrade?

Yes, please check your email.

>>3) What is the version of the current source license (is it 4.0 or 4.5)?

4.5.0.1.

>> What is the upgrade policy for this license (Source code license)?

Please check your email.