Auto Transmission problem....

Hi Guys, I own a MK1 octavia (1.6) which I bought with a busted auto transmission. I replaced this with a spare transmission from a junkyard. On my first test drive with the replacement transmission I noticed the gear changes were slighty "jerky" and the car felt a bit down on power.  I assumed this may have been that the transmission was a bit low on oil, however before I was able to top up on oil, I noticed that the rear crank seal was leaking so I had to take the transmission down to replace it.

Warning ! This may be a bit of a read....

Problem 1

So while replacing the seal I decided to replace the stock auto cooler with a front mounted transmission cooler that I got off of a ford focus....and this is when all the problems began. While the car is idling in park I hear a hiss coming from the focus cooler and it sounds as though air is in the system. So I rigged up a simple T connection on the exit/ return of the focus cooler in an attempt to bleed the air out. I tried bleeding the system for about 1 minute  but air still remains in the system as though the bleeding process has no effect on it. At this point I got fedup and tried putting the car on drive while on jack stands. I realised that I needed to rev the engine up first before the wheels started to spin on drive. When this new problem came up I decided to check the fluid level. I had the car up on four jack stands level to the ground, removed the drain bolt on the tranny, started to pour ATF fluid into the filler until oil started to leak out of the drain plug. It used a little less than half a quart of oil to fill the transmission. While still on jack stands I put the car in drive and the wheels started to spin immediately. At this point I though problem solved!

With the car off the jack stands, on the ground, I realize that it still needs a slight rev before it can move in drive or any other gear except for reverse. As soon as i put the car in reverse, it moves instantly without me having to give it gas. However whenever I am in a forward gear without giving it gas, the car rolls forward a couple feet the stops for a couple seconds then rolls forward again a couple feet stops and repeats like this unless I give it gas. I was assuming this was a result of still having air in the auto cooling system but why does it work fine on the reverse gear?

Problem 2

While I had the car off the ground replacing the transmission, I decided to change my rear drum brake to disc brakes. I took a rear suspension off of a MK4 Bora and swapped it into my octavia. Fortunately this was a relatively straight forward swap. I bled the entire brake sytem starting from the master cylinder working my way throughout all the wheels. The pedal feel was great...until I started the car. The car started to "hunt" as though there was a vaccum leak and the brake pedal went almost to the floor. Upon further inspection I noticed that the booster vaccum line had cracked. I replaced the line but the same problem persists, however now the "hunting" idle has become intermittent. I have checked for other vaccum leaks throughout the engine by using soap water but so far I wasn't able to find any.

I am not sure if this related to the first problem or if this is the cause of the first problem as I did not have any of these problems before I dropped the transmission to replace the seals. I am not sure if I may have overlooked something but at the moment I am a bit lost and fustrated. Do you guys have any ideas or suggestions on this?