Don,
Having owned both amps, I can tell you there are differences.
The VT 100 MK II is a solid all around performer. Nice extension, good 'staging, quiet noise floor and good dynamics. It is also a pain to bias, "needs"* expensive ARC matched output tubes and has a fan that some find objectionable to listen to. I never heard the fan during music play but it does make some sound.
The VTL is to my ears a more coherent sound. Less dry on the top and and has a touch more space and "air" in the 'stage. Bias setting is a snap and does not require matched tubes. VTL does recommend their own tubes but they are a lot less spendy than the ARC tubes. That being said, the VTL does not have XLR inputs and that is why I am selling mine. It is the latest version for sale on the 'gon used section.
The Mod 3A is a killer pre with plenty of voltage to drive either amp. The Vanersteen 2Ce Sigs are a huge value and hard to top for under $5,000.00. Either amp will drive them well. IMHO the VTL is a clearer picture into the music and recording. YMMV.
* I have heard and read a ton of discussion on the ARC tube replacement stance so please do not start a flame war (meant for the ARC die-hards, not the OP). I am just passing along what ARC has told me personally.