WR 426 bizzare issue

So this is my first actual post on TT as I usually am able to find previous posts addressing topics I am searching for. However, I have been unable to with this one. Recently I pulled my 2001 WR 426 out to go for a weekend of riding. I hadn't ridden it in a few months and took the carb off and cleaned everything really well and put it all back together and went to start the bike. It took forever for the bike to start and once it did it wouldn't run without the choke being on. I rode the bike down the road and back with the choke on hoping to get it to smooth out. Long story shorter, It ended up looking like I had skipped time by a tooth or two. I had a friend look at the bike with me and since my weekend was ruined I went and got a new timing chain, top end gasket kit etc. and installed it. I also leak tested the head while it was off. Put it all back together and Althogh the timing marks are not perfect they are as close as humanly possible. When I went to start the bike after the install the kick starter is bottoming out about 2-3 inches before reaching full stroke. I took the spark plug out and it kicks full stroke. Also while kicking the compression release is not needed although there is still enough compression for it to run. I am no mechanic and am a bit at a loss. I would think bent valves but the head passed the leak test and the top pf the piston looked flawless, but me and a few friends I have had give it a look can't figure it out. Any help would be appreciated or if someone would loan me a bazooka I could take care of it real quick. By the way the bike before this ran well, especially once I unhooked the TPS.

this compression loss happened to me and it ended up being bad rings. did you torque down the head to the right amount?

Sounds like your cam timing is waaaaaay off.

I had a similar issue which turned out to be a seized de-compression cable holding the valve open and stopping me having any compression.

Make sure its operating smoothly and not sticking.

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