Specifically regarding the Part 61 vs. 141 question...
I've found that doing your Private under 61 is better than than 141. This means you don't necessarily have to go to a larger flight school and pay their premium prices, and rather find something more affordable per hour. If I'm not mistaken, the 141 minimums for a Private certificate are 35, as compared to 61 minimums of only 40. With the average closer to 70 (or more, depending on where you train), there is little 141 advantage.
Now for your Instrument rating, a 141 course is valuable because it eliminates the 50 hours cross country that would be required if you do it under 61. Also, generally Instrument training with a 141 syllabus is very effective (more so than with a Private certificate, where the instructor has more flexibility), which can be a plus. Doing your Commercial 141 brings the total time requirement down to 190 (as opposed to 250 under 61), however, up to 50 hours of Flight Training Device time can be used towards the 250 total time requirement under 61. So, all things considered, if you can get cheaper per-hour rates flying somewhere 61, for your Commercial that may be your best bet.
As far as VA benefits, well, factor that into your decision making. If it's true that they only apply after your Private, than starting 61 and then doing your Instrument and Commercial 141 would make the most sense.