Hi Can you Generate AutoIdentity Number(adding new ID columne/through Script Component) for Each File Seperately.

Then Apply Merge Join , Based on ID Column(this helps Join on RowNumber Position)

example:

File1

Id Col

1 A

2 B

3 C

File 2

Id Col

1 D

2 E

3 F

Merge Join On File1.ID = File2.ID

So Final out put will be

ID File1.Col File2.Col

1 A D

2 B E

3 C F