Engine 1986 GT block prob

Greetings, all:

I have a serious problem with the 86GT. Summer 2017 while drilling out a broken water pump bolt, I drilled into the water jacket and of course coolant flooded out. The repair included a sealant and a time-cert thread repair. Actually worked fine until about a week ago. Timing cover gasket is now green instead of blue- the part that sticks out and is visible. And coolant is seeping out the passenger side valve cover. Clearly a head gasket failure and aforementioned hole failure.
I need advice- the engine was rebuilt about seventeen yeas ago and only has 80,000 miles on it. Plus the compression is still good. I was trying to figure out why the stat took twelve minutes to open. Now I know. I shut it off before total failure although it wasn't close to overheating.
Is it worth repair and do I need another rebuild? I know these blocks were somewhat thin to begin with so as it is already .030 over...
I'd rather just repair the hole. Its the lower of the two holes on the passenger side of the engine the timing cover/ water pump mates to.
It will need re-drilled, welded, tapped, etc. Plus the head gasket thing.
A real shame as I've repaired some minor problems like oil seeps and timing and idle issues. Last trip it ran great and was more fun than usual.
Its a keeper although not a looker. Needs painted, too.
Thoughts and ideas? Much appreciated. Other boards are just critical.
Thanks and Merry Christmas. Happy New Year as well.
Cheers.

Included are some pictures. I removed the upper intake and passenger side valve cover today. I saw some rust on one valve spring. No coolant anywhere. Lighting from the camera makes it appear there is more rust but there is none. It looks very good under there. The first picture is about where the cover gasket leaked when I put it on last summer. I re-tightened it after repositioning the cover but maybe the gasket is not good, not sure. The leak stopped. When I thought there might be coolant leaking in the same spot, I can't actually say it was coolant. Not sure where the rust on the spring came from. All the rest are good. I did notice the gasket between the throttle and EGR spacer looks to have leaked in the past. Much crystalized coolant around it. Plus a small puddle of coolant in the lower intake manifold directly under that spot. No other leaks or residue found. No coolant in engine oil on dipstick either. No cracked head or freeze plugs. Puzzled.
Perhaps the TB gasket leaked and allowed air into the cooling system, putting air behind the thermostat and keeping it from opening until after twelve minutes?
Definitely will replace the TB gasket, and probably the valve cover gasket to be safe. The TB gasket has leaked before. Unfortunately the surface of the TB that mates with the gasket is not quite smooth. I had no compression problems and the car ran fine when I tested all this about two weeks ago.
Doesn't appear to be head gasket at this point but I hesitate to try again and really damage things.
Thoughts everyone? Thanks much.
Here's the rust.

I wouldn't mind removing the engine and checking things out but with only 80,000 miles and running sweet, until the coolant/ thermostat/ possibly overheating problem recently, and WInter weather here now- no garage- I'd like to let it be.
Cheers.

Managed to replace thr throttle body gasket and get everything back together last week. Cleaned up nice. Due to the cold I can't repair the block leak under the timing cover until I get a little warmer air. When I do I'll keep everyone posted. Might be a while though...

And the valve cover gasket. Forgot that one.