It is nearly impossible to fix a leak with material - metal, roofing cement - applied to the outer surface. Water will inevitably find its way beneath the superficial coating. The condition of the shingles in the photos indicate the need for a new roof anyway. This is really the only and best long term solution/

The entire roof of the main home and the addition (and some siding) needs to be removed and replaced. And CORRECTLY FLASHED. What's there was never done correctly from the beginning. If it's been leaking for years, you may have some major structural damage to repair as well. You're definitely going to have to replace some of the sheathing in that area.

Replace it all properly.

What a mess! I agree with most of what has already been said but I have a feeling you are looking for a way to halt the leak or at least slow it down a lot until you ship come's in. Every time I see this type thing the first thing I would like to do is have the responsible parties come clean their dirt daubbering off so it doesn't prevent fixing the origional screw up when the roof was installed. I figure where the valley dumps is causing most of the problem eventhough some of the water doesn't get inside untile farthur down. I think getting the water to fall farthure out will help a lot. When you install or repair roofing think about the huts in 3rd world countries and how the roofs are constructed. No caulk or other means of plugging holes. Water runs of each leaf onto the one down hill,beside and underneath it. Same principle with our wood shake roofing. From inside the attic of a wood roof there is so much daylight everywhere it's seems impossible the roof doesn't leak in a thousand places,until you think about the thatch roofed huts. With that principle in mind,you will do much better roofing. Ok,let's try and slay the biggest culprit. In the 2nd,3rd and 4th pics,work a piece of flat metal under the open valley metal. To size the metal,use a long 2" putty knife to feel underneath the valley to find maxium width and how far up you will be able to insert new metal. Add as much as possible to overhang the metal lower roof. Be extremly carful about cracking shingles in the valley because it will leak horriably. Any damage in the valley should be repaired with ASPHALTIC,non hardening roof patch "tar" for the lack of a better short name. DO NOT apply tar at lower most seam where valley overlaps new metal eventhough the shingle tips were likly broke while opening access to add new metal. REMEMBER the thatch hut effect plus if water gets between the valley and new metal,you want an escape route instead of sealing it in. If you must pull a nail to alow path for new metal,doctor the nail hole with a dab of tar. Don't worry with nailing the new metal if you can have friction hold it in place.
I have to run errands for 3 or 4 hours be fore getting back to you,smoke on this and see if we are on the same page.

denaliakitas:

You fix this roof with a banker and a reputable roofing contractor, not hand tools and goo.

I know this isn't what you wanted to hear, but I have to give it to you as I see it.

Klem1!
Thank you for your post. I would appreciate more follow up greatly! You are correct that i am needing to get this temporarily fixed until next late spring early summer when i will have the time/money to have it taken care of properly.
I am following you on extending the valley flashing. I was thinking about possibly scraping as much of the roofing cement off as possible and then using an elastomer coating with reinforcement cloth in the critical areas. What do you think? THanks