I used Spank's advice and moved one bearing half from the center to rear. I cleaned every journal, cap and bearing twice and scrutinized every component and put it together using plastigauge. and all the tolerances are within spec. (.0015in). Cleaned every component again put it back together and the crank now spins good with no hick-ups. 

Thanks for all your input and suggestions. You guys are the bomb, as always.

Free money is to swap around the bearings to different journals and recheck, rub some green scrubby around the block journal prior to snapping the bearings in. What I try to do when using plastigauge is to always tighten up the main bolts to spec then just undo one cap at a time (leaving the others tightened up) and plastigauge just that one journal to check its clearance. If it proves tight or loose, rotate crank 90 degrees and check it again. Then move on to the next.

I like plastigauge because it is user-friendly, can be done at home with no other special tools, and it can give a preliminary check for a bent crank without the need to succumb to the schedule of a machine shop.

If there is a problem with mismatched sizes, I'd suspect the crank over the block especially if it's tight. If it were LOOSE on one journal, I'd wonder about the block.

Don't step back , Steve, your advice and insight is always welcome in my book. As well as eveyone, with few exception.

I was going to talk to my machinist about this issue and most probably take the block, crank and bearings over to him for a look see.

I did have the center cap on right way round figuring that if the font and back caps were that way (bearing tangs on the same side) then the center should be.

I have another 1100 block and crank.

I let you know how it goes.

No you don't need 50 years on the job to do a good job. You also should not over look the resource your local machine shop can be. Checking line bore for align takes a couple min. measuring housing bores is quick and a ball mike will give bearing thickness. Do the math the way it's meant to be. Mashing a section of wax is a rough check. We now know we are tight, who's tight?  We don't know. Just a suggestion I'll step back. Steve (CTR)

Plastigage is a great resource, especially in this instance where there was and still may be confusion with the caps.

A person does not need fifty years of experience to build an engine, just a desire to do good work and check things as they progress. It could be that the machinist line bored it with the Center main turned around, maybe that was for the thrust surface or some other motivator.

If you are not sure about the center cap the bearing locking lips / tangs both go on the same side next to each other. I have been building engines since 1965 and have never had or used plastigauge. Take the block, crank and bearing to the machine shop. They will have the proper mikes to measure crank, block housing bore and bearing thickness with a ball mike. You need to understand indexing the crank and removing the very small amount is just about impossible. One might think that small amount could be removed with a polishing belt. While a polishing belt is good to polish it does not remove metal evenly. Line boring the block again with a new or different cap will move the crank closer to the cam putting slack in the timing chain. My suggestion would be have the shop that line bored help you sort the issue or buy a good A+ 998 block and work with that. I have a 1100 block bare but need to look at the condition. I'm currently building two over bored 998 s with A+ blocks, A+ press fit rods balanced with light steel flywheel,  two part Cooper S balancer and 295 cyl head with hard seats O/S valves and one with SW 5 and the other yet to pick a cam. One is pre sold the other is for sale after I play with it. Thinking maybe MG Metro cam and twin 1 1/4 SUs with the small Cooper header. Steve (CTR)  

Sounds like you will have no problem figuring this out. Cool build, I have a big 998 coming together, +0.080 Russel pistons. 

Crankshaft is .020 undersize, bearings are Glyco H1310/3 0.5MM on the box (0.508 on bearing itself), block was line bored because I wasn't sure what caps were from what disassembled engine they were from (2 MG 1100 engines disassembled years ago ), I could have the center cap on 180 out, I didn't see any detritus, I have a center strap on order, I will have to mic the main bearing for roundness, and use plasticgauge on three areas as you suggest after inspection and cleaning. I though the engine looked good and so did my machinist. Crankshaft was ground by another machine shop.

I will check every comment out. 

I am building a 1218, trying to follow the Graham Russell build.

Has the crankshaft been ground undersize? What size? What size are your bearings? Was the block line bored? Were the main caps mixed with another engine? Are they fitted correctly? Did you machine the main cap for a center strap? Have you checked for detritus where the bearings sit in the block or in the cap? Is the main bearing even round? Did you lay plastigage in at just one point or did you measure a few places? What did things look like when this engine was dismantled?

I just measured my crankshaft running clearances with plasicgauge and got the following:

#1 (front) bearing  =  .0015 in
#2 (center) bearing = .00085 in
#3 (back) bearing = .0015 in

Haynes list tolerance as .001 to .0027, so the center bearing is a little tight. Will this work or do I need to figure out a fix (grinding a little off the journal)?

Thoughts?