No, the switches need to be removed from the board in order to do a jailhouse mod.
Blues will likely be fine if you have a loud office, or an area where you can close your door. They have the added advantage of making you sound more productive

Some people find that the caps you use with blues can alter the sound slightly, although probably not enough to make a difference.
If you are concerned about noise, blues will likely be an issue, because of their high-pitched click. I have not personally tried gateron switches, but the general consensus is that the gateron browns are smoother than their cherry counterparts.
I'm not sure what you mean by you have "caps, springs, lube, case, etc." That sounds more like a list of parts for building a board than anything else. If you are planning to mod your board, swapping springs and lubing switches also require desoldering on that board. Depending on your case, changing the case may also require desoldering. If you really want clears, why not order a bunch of clears and swap the switch out at the same time you do some of those other mods?