HSMXpress depth of cut too deep?

The parts are all milled from Alco 5 tool plate at 1/4" thickness. They are upgrade parts for the hot end mounting of a SeemeCNC Rostock Max or Orion 3D delta printer.

I would look into the following mod fist over printing anything for stiffing: A 30 minute x-axis mod to reduce chatter. It is a very simple mod which is very cheap and easy to install. I did it but added a strip of 1/8" steel on the bottom plate in addition to the washers and it has been a great mod and REALLY reduced chatter.

I use a simple 12V blower fan to clear the area of my cuts. the fan costs around $5 from Sparkfun: Blower - Squirrel Cage (12V) - COM-11270 - SparkFun Electronics with a few simple 3D printed parts and some loc line ($12ish on amazon) you can run the mill for 9+ hours cutting 1/4" stock without chip clearance issues.
You can see a bit more about it and how well it works in this post: Production level aluminum milling with .8KW water cooled VFD

As far as bits go. I have yet to find a better bit than the 3 flute Destiny Tools Viper end mills. I have them in 1/8-1/2" and love each one. They mill perceftly and produce a MIRROR finish on the parts with just one simple finishing pass. I use the same end mill for everything and just do a double finishing pass of about .125MM in HSM and it gives an amazing result. They can be found cheaply from this seller on Ebay ( he sells great end mills over all) http://www.ebay.com/itm/1-8-carbide-endmill-for-aluminum-milling-coated-3-flute-Destiny-Tool-V30805S-/151851495498?hash=item235b0df04a:m:mB6EV486fHjorKMn2EtgwMw

I would stick with either the Solidworks like you do now (which is what I use also) or with Fusion360. Fusion360 uses HSMworks at their CAM. Only other software Iw ould suggest would be MESHCAM and maybe the Aspire V carve or Aspire 4. Aspire does a great job of engraving with V bits which oddly enough HSMworks is not so good at.