I have thinned down at least a dozen shell holders over the years. I take off .006-.012 to eliminate the "caming over" of the Rock Chucker press. Since the bottom of the sizing die never touches the top of the shell holder if you have taken off enough, canted top shell holders are not an issue, within reason. Shell holders are hardened, using sandpaper is a tedious process. I have a fine wheel on a 6" bench grinder, and very gently hold the shell holder up against the side of the bench grinder, carefully with little pressure. I dip the shell holder in a cup of water frequently, then measure with a pair of calipers. Always wear safety glasses and/or face shield when using a bench grinder.
You will have to take .035+ off the top of the shell holder before the shell holder becomes useless, so just measure the shell holder thickness frequently with .003-.006 removal off the top being sufficient. The most I have ever had to take off the top of a shell holder is .013 for rifle cartridges, Lyman, RCBS, and Forster which is a deep subject in and of itself. I was trying to make a sizing die work that was reamed too large, so production dies do vary in size.
Only one shell holder did I have to grind down thin on the top and that was to size the bulge out of 40 S&W brass or take more bulge out.
Taking the material off the bottom of the Die is a really bad idea, for many reasons, and is ill advised.
CBuck516, you have another problem with your 25/06 AI, and that is using Lapua brass. Many do not understand that European Brass is made to CIP spec and American brass is made to SAAMI spec, in some cartridge configurations. The CIP spec brass is often larger in the web, just in front of the extractor groove, and often this brass simply does not work in the SAAMI spec chambers. So this means that Lapua, Norma, and RWS brass maybe too large in the web to be used in your SAAMI spec chamber. Chances are that if you Change to Winchester brass, new Lake city Match '06 brass, or Remington brass, your problem will be solved. However, we do like to use the best brass when we have that option.
I ran into this exact same problem with Custom Chambers in 223, 22/250 AI, 243, 243 AI, and 22-243 AI. Factory chambers are much looser and Headspaced longer than Custom barrel chambers as a rule of thumb, which explains why some std calibers in Lapua brass can be used in factory guns and NOT custom..
If you are dead set on using Lapua brass in your 25/06 AI, then a gunsmith can remove the barrel, put it in the lathe through the headstock, and "polish" out the chamber a tad. SOME gunsmiths have CIP and SAAMI spec reamers, and PTG and JGS Reamer makers are familiar with this problem.
Question: Your Lapua New brass Web dimension on the Lapua 30/06 brass is___________,
New Winchester Web dimension is .465, which I have on hand
while the fire formed Lapua brass web dimension is__________,
and the Full length Lapua sized web dimension is__________.
Taper on the AI case is very little, and you may not achieve the dimension in the web you are looking for by removing metal off the shell holder and your darn sure will not get there by taking material off the bottom of the Full Length sizer due to the body taper involved.
On some AI's, I have cut the bottom off of a Small base sizer of the parent case, ending up with a "ring die" that is only about 3/4" long to size the bottom of the case only. These ring dies are complicated and expensive to make with sometimes less than desired results. Other options give a more harmonious outcome, like Winchester brass. A carbide-tipped cut-off blade used in a lathe is needed for cutting off the Hardened full-length sizer. Having your gunsmith make "ring dies" is a mess to get involved with just to obsess over having to use European brass, but I have done it on more than one barrel, and it is ill-advised.
CBuck516, if you measure the web dimension on new Winchester brass and New Lapua, you are going to be in for a real shock at the difference in dimensions with the Winchester being MUCH smaller, eliminating jumping through any hoops on the issues of shell holders, ring dies, gunsmith polishing out the chamber, etc.