Transmission will not go in. HELP!!!!!

I am converting auto to 4 speed in a 1970 dart 340,I have all the parts and pieces, my problem is after installing flywheel, clutch disc and pressure plate and bellhousing. the transmission will not go in. The bearing retainer hits the bellhousing. I checked the alignment and it was off, so I bought off set alignment dowls 21 th. the largest offset available and and the retainer still hits. I took the dowls out and and put 3 bellhousing bolts in and the trans slides right in. I put the rest of the bellhousing bolts in ,all but 1 that was off just a bit . Has any one had this problem? I have been fighting this for a couple of months now and am at witts end. Can you run without the dowl pins in?