Hello and welcome.
It sur eis a pain to mount Mugen and the ASUS Rampage Formula, they both have their limits and then there is not much space left. You definitely should remove the Mobo first, mount the Mugen, then put the whole thing into the Case. That is the very easiest way for this combination.
- I can supply you with a new set of Push Pins clips but I would rather recommend Option 2 for your system
- Get a Universal Retention Kit or the Thermalright Bolt Thru Kit, which ever you want to go for, yet I can not give you a strict advise for TR Bolt Thru Kit, as I did not test it on my own and it is "modding" of clips. Then use the supplied socket 478 clips for Mugen to mount it on the Universal Retention Kit. It is a very solid mounting and should save you some