to answer your questions
1- In the documentation it is mentioned that LLBLGEN Pro is used for the DAL. Which version is used of LLBLGEN? What was the framework? v1, v4, LINQ TO SQL, Runtime Framework or NHibernate? It is important to mention even in the documentation as if anyone want to modify the existing web parts, all these information are very important?
Documentation was written in the period when LLBLGen 2.6 was the latest version and now MonoX is using LLBLGen 3.1 which has a bit different concept (from the visual designer point of view) so we will update the MonoX documentation in next release. So LLBLGen 3.1 is used in Adapter mode with LLBLGen Framework compiled for .NET 4.0.
2- It is mentioned in the documentation that LINQ can be used? The syntax of LINQ and LLBLGEN is different? If we create LINQ to SQL code from LLBLGEN, wouldn't it be LINQ Code?
LLBLGen to Linq concept is the same, the only thing that you need to do is to create the DataAccessAdapter and LinqMetaData from there on you have strongly typed data objects and pure LINQ e.g.
using(DataAccessAdapter adapter = new DataAccessAdapter())
LinqMetaData metaData = new LinqMetaData(adapter);
var q = from c in metaData.Customer
// enumerate over q here so it gets executed
Please take a look at the following articles
Generated code - Linq to LLBLGen Pro, getting started
Generated code - Linq to LLBLGen Pro, Prefetch paths
Developing Linq to LLBLGen Pro, part 1
(Series of LLBLGen to LINQ articles)
3- If i create seperate project for the sake of creating new web part using LINQ. What files will go to repositories folder and what files will go to BusinessLayer folder?
Please take a look at the following articles to see the above patterns (Note: there are many articles describing the Repository and BLL patterns)
The Repository Pattern
Business Layer Guidelines
Let us know if you need anything else.