When I did my ATS manifold I had the same problem with the cap bolts provided by ATS not holding torque. I got with RustyJC and he did some thermo dynamic analysis of manifold growth with heat, elastic configurations of bolts and studs, and torque retention.
Bottom line, use factory bolts on all but #3 & #4 top (can't use factory because the ATS manifold passages are larger than stock). On #3 & #4 top use studs and Belleville washers and Drake Lock Nuts. The Belleville washers are also called cone washers. They will deflect (cone gets flatter) as the manifold boss heats. However when the boss cools they go back to their ORGIONAL shape. Therfore the torque will hold correctly. Each Belleville will distort about . 0015. The manifold will grow in thickness about . 0035, therefore you need 3 Belleville washers. The stud I used was a 52mm. Length is important as the elastic (ability of the stud to stretch AND return to its orgional length) nature of the stud is part of the clamping equations. Then Drake Lock nut that will not rotate because the 2 parts of the lock nut prevent either part from rotating.
If you just torque a stud in without the Bellevilles the stud will be stretched too much and will go plastic (will stretch but WILL NOT return to its orgional length) and the torque will not hold. If you try to retorque the stud to hold torque eventually you will break the stud off in the block.
In the archives there is a very long thread about this. I installed my ATS manifold and had cap bolts fall out. Then the TSB about using the dog bone stainless steel retainer came out and that workes for everything but #3 & #4 top. The reason the OEM bolts are so long with the heat shield sleeve is that with a bolt that long it has a longer elastic limit and can grow and shrink along with the manifold growth and shrink cycles as the manifold heat cycles.
When I did mine I first put the studs and Bellevilles on ALL the studs. Then the TSB came out and I reduced mine to the #3 & #4 top. Therefore I have several sets of the studs and Belleville washers remaining. I have slowly sold all but 6 sets of them off. Each set is $45 (which is my cost) plus shipping to wherever you are. I had a heck of a time finding an industrial reseller that would sell me just a couple fo the Bellevilles. Most wanted me to buy lots of 1000. The Belleville were about $10 EACH * 3, + Drake Lock nut $10, + stud $3, + a couple of stainless steel washers $1 *2, so the Bellevilles do not cut into your ATS manifold or Drake Lock nut.
You can go back and read the threads, search for "Belleville washers".
Bob Weis