Can you help me understand how you get the gun separated from the leg? Which part do you remove material from / cut through with your jeweler saw?
I use a jeweler's saw with a 3/0 blade... Please remember, all saws "eat" material. The almost hair width of the jeweler's blade keeps this to a minimum, while the short height also allows you to maneuver the blade while cutting. Downside is that the 3/0 blades are fragile and snap easily (sometimes, too easy), which is partly why I don't move to a 4/0 blade...
As for cutting, I come at the laser from where the barrel meets the leg and try to cut the front of the shin flat. Same holds true for the knee... The front of the shin requires just some light cleaning up, but not much else, and it give you some material on the side of the knee to shape with a file... Next, I angle the blade some, maybe between 30 - 45 degree to the lower thigh, which requires more clean up to flatten it, but leaves more of the gun behind... Note: if you look at the left leg, you will see a cone-shaped detail on the side of the leg. This exists on the right leg too, it is just kind of hidden from the front view by the gun. I would suggest matching the angle of your cut to match the slope of that detail. Yes, you will chew up a bit more of the gun, but I think it is worth it... Also, if you do not plan to move the upper shoulder (I don't think I did on either of the first two 23rd Arcturan Guards ones), then a trick I sometimes use is to undo one end of the blade from the jeweler's saw, feed the blade through the arm, and the reattach it to the saw. This allows me to cut from a slightly different angle and sometimes makes it a little easier.
I can only assume that the arm will be cut somewhere else (shoulder, elbow, somewhere) so that it can be repositioned. Otherwise this is a lot of work just to have the gun not be attached to the leg... So once the arm is off, I shape the knee, clean up the shin and the lower thigh, as well as that cone shaped piece... Typically this involve a little green stuff too... I also rebuilt the gun, adding back details, and then I file the front barrel round and drill out the tip... Also, just below the left knee there is a trapezoidal little detail. I tend to add that back with a little green stuff too.
For this last one, I also cut the gun completely away from the arm... Do do that, I cut even with the top of the forearm (much like I did the shin), but made a 90 degree turn and cut the hand off. I then filed down the fin portion of the gun on the inner forearm... Doing this let me rotate the hand, and by leaving the hand in tact, I had a place to insert the pins.
Finally, if you've never worked with thin parts before, I suggest looking into .015 and/or .020 music wire (I think the old wire antenna material was .015 music wire)... This stuff is pretty stiff and much thinner than paperclips, which means that you can drill in your pins without eating almost all the surrounding material. On my 9th Marik P-Hawk, I managed to get two pins in everything, including the hand, during reassembly (I double pin every part I can, so that the part can't rotate around the pin and break the glue that way)
I hope all this makes sense, and if you need something clarified, don't be afraid to ask.
Caz